[ccp4bb] Fwd: [ccp4bb] Crystal optimization

[Nicholas Clark]

Apologies, my response was directly to the OP and not to the BB. I have
forwarded the response to maintain the chain.

-- Forwarded message -
From: Nicholas Clark 
Date: Fri, May 31, 2024 at 7:23 AM
Subject: Re: [ccp4bb] Crystal optimization
To: 白雪慧 


I had a protein that no matter what we did, only grew urchins very similar
to what you’ve shown here. Even with extensive optimization, we were only
ever able to grow urchins.

Ultimately, the only way we were able to grow diffraction quality crystals
and allowed us to solve the structure (with resolution ranging from 1.4-
2.2 angstroms, depending on ligand) was using MMS, as Tom suggested.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157405/

Best,

Nick

Nicholas D. Clark, PhD (He/Him)
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203


On Thu, May 30, 2024 at 10:34 PM 白雪慧  wrote:

> Thank you very much for your suggestions. I have a question. My crystal
> grows microcrystals under multiple conditions, as shown in the figure.
> After orthogonal optimization of the precipitant and pH, the crystal growth
> is still very small and difficult to obtain diffraction. What is the method
> to optimize and increase the crystal size in this situation?
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>


-- 
Nicholas D. Clark, PhD (He/Him)
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203



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Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Wankowicz, Stephanie]

If it does what it claims – incredibly impressive. The issue we have is there 
is no way to verify or validate the claims it is making.

The letter is a call and start of a conversation about how the ever-changing 
landscape of communication and publication of science should be.

-Stephanie Wankowicz

From: CCP4 bulletin board  on behalf of Krieger, James M 

Sent: Monday, May 13, 2024 10:22 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

It definitely is impressive but it also has clear limitations On 13 May 2024, 
at 15: 22, Sylvia Fanucchi <d0c4e77ae410-dmarc-request@ jiscmail. ac. uk> 
wrote:  You don't often get email from d0c4e77ae410-dmarc-request@ 
jiscmail. ac. uk. 
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd
It definitely is impressive but it also has clear limitations

On 13 May 2024, at 15:22, Sylvia Fanucchi 
<d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk> wrote:


You don't often get email from d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is 
important<https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AmVluUFn$>
Is it just me who is really impressed by it? Am I missing something?

Get Outlook for 
Android<https://urldefense.com/v3/__https://aka.ms/AAb9ysg__;!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7ArXNQatL$>

From: CCP4 bulletin board  on behalf of Rafael Marques 

Sent: Monday, May 13, 2024 3:13:16 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was 
preparing to submit my second job, the first one was already finished, which 
made me think that I was definitely doing something wrong. Probably I was...

Best wishes

Rafael Marques


On 13 May 2024 09:53, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz 
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
>
>
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
> <https://spam.ic.ac.uk/SpamConsole/Senders.aspx><https://urldefense.com/v3/__https://spam.ic.ac.uk/SpamConsole/Senders.aspx*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AkQKssvO$>
>  to disable email stamping for this address.
>
>Hello,
>
>
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work.
>
>
>
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
>
>
>
>Please see the entire letter here. 
> <https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link><https://urldefense.com/v3/__https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AqTp0-CX$>
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form.
>
>
>
>Additionally, a PDF version of the letter can be found here 
> <https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing><https://urldefense.com/v3/__https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing*3E__;JQ!!LQC6Cpwp!ojUwuRRzsCarUF-wwnVWIQtQbTonf10zBas4dHDOMDcNF3qWUSO99i3QLLB39nBZ8NEnc9RG_drv9T5at5d7AmjNPgIH$>.
>
>
>
>Thank you,
>
>
>
>Stephanie Wankowicz, UCSF
>
>Pedro

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Krieger, James M]

It definitely is impressive but it also has clear limitations

On 13 May 2024, at 15:22, Sylvia Fanucchi 
<d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk> wrote:


You don't often get email from d0c4e77ae410-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Is it just me who is really impressed by it? Am I missing something?

Get Outlook for Android<https://aka.ms/AAb9ysg>

From: CCP4 bulletin board  on behalf of Rafael Marques 

Sent: Monday, May 13, 2024 3:13:16 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was 
preparing to submit my second job, the first one was already finished, which 
made me think that I was definitely doing something wrong. Probably I was...

Best wishes

Rafael Marques


On 13 May 2024 09:53, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz 
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
>
>
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
> <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping 
> for this address.
>
>Hello,
>
>
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work.
>
>
>
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
>
>
>
>Please see the entire letter here. 
> <https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link>
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form.
>
>
>
>Additionally, a PDF version of the letter can be found here 
> <https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing>.
>
>
>
>Thank you,
>
>
>
>Stephanie Wankowicz, UCSF
>
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, UCSF
>James Fraser, UCSF
>
>



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#

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Sylvia Fanucchi]

Is it just me who is really impressed by it? Am I missing something?

Get Outlook for Android<https://aka.ms/AAb9ysg>

From: CCP4 bulletin board  on behalf of Rafael Marques 

Sent: Monday, May 13, 2024 3:13:16 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was 
preparing to submit my second job, the first one was already finished, which 
made me think that I was definitely doing something wrong. Probably I was...

Best wishes

Rafael Marques


On 13 May 2024 09:53, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz 
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
>
>
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
> <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping 
> for this address.
>
>Hello,
>
>
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work.
>
>
>
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
>
>
>
>Please see the entire letter here. 
> <https://docs.google.com/forms/d/e/1FAIpQLSf6ioZPbxiDZy5h4qxo-bHa0XOTOxEYHObht0SX8EgwfPHY_g/viewform?usp=sf_link>
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form.
>
>
>
>Additionally, a PDF version of the letter can be found here 
> <https://drive.google.com/file/d/1u1D3KzsllpI_6I0drA9RdIiENd9EK1Hz/view?usp=sharing>.
>
>
>
>Thank you,
>
>
>
>Stephanie Wankowicz, UCSF
>
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, UCSF
>James Fraser, UCSF
>
>



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and recipients are thus advised that the content of this message may not be 
legally binding on the University and may contain the personal views and 
opinions of the author, which are not necessarily the views and opinions of The 
University of the Witwatersrand, Johannesburg. All agreements between the 
University and outsiders are subject to South African Law unless the University 
agrees in writing to the contrary.



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Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Rafael Marques]

I tried it yesterday and I was really shocked by how fast it is. When I was preparing to submit my second job, the first one was already finished, which made me think that I was definitely doing something wrong. Probably I was...Best wishes Rafael Marques On 13 May 2024 09:53, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:Hi folks



This arrived in my inbox this morning, and I believe that it may provoke some discussion…



Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν



Best wishes!



Harry



>    From: Stephanie Wankowicz  

>    Sent: Saturday, May 11, 2024 3:31 PM

>    To: James Fraser ; Pedro Beltrao ; Benjamin Cravatt ; Roland Dunbrack ; Anthony Gitter ; Kresten Lindorff-Larsen ; Sergey Ovchinnikov ; Polizzi, Nicholas F. ; Brian Shoichet 

>    Subject: AlphaFold3 Transparency and Reproducibility

> 

> 

>    This email from mullane.stepha...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list  to disable email stamping for this address. 

> 

>    Hello,

> 

> 

>    As many of you, we were incredibly disappointed with the lack of code or even executables accompanying the publication of AlphaFold3 in Nature. AlphaFold3 was released without the means to test and use the software in a high-throughput manner. This does not align with the principles of scientific research, which rely on the ability of the community to evaluate, use, and build upon existing work. 

> 

> 

> 

>    We have written a letter, which will be posted on Zenodo and submitted as a Letter to the Editor in the coming days.

> 

> 

> 

>    Please see the entire letter here.  If you want to endorse this letter, please fill out your name, affiliation, and email in the form. 

> 

> 

> 

>    Additionally, a PDF version of the letter can be found here . 

> 

> 

> 

>    Thank you, 

> 

> 

> 

>    Stephanie Wankowicz, UCSF

> 

>    Pedro Beltrao, ETH

>    Benjamin Cravatt, Scripps

>    Roland Dunbrack, FCCC

>    Anthony Gitter, UW Madison

>    Kresten Lindorff-Larsen, Copenhagen

>    Sergey Ovchinnikov, MIT

>    Nicholas Polizzi, DFCI/HMS

>    Brian Shoichet, UCSF

>    James Fraser, UCSF

> 

> 







To unsubscribe from the CCP4BB list, click the following link:

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Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Pedro Matias]

Hi Harry,

Thanks for sharing this. I already read and endorsed the letter.

However, I do have a comment - since one of the letter signatories was a 
reviewer of the paper, wouldn't the shortcomings described in the letter 
be grounds for rejection of the manuscript?


Best regards,

Pedro

On 13/05/2024 09:53, Harry Powell wrote:

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry


From: Stephanie Wankowicz 
Sent: Saturday, May 11, 2024 3:31 PM
To: James Fraser ; Pedro Beltrao ; Benjamin Cravatt 
; Roland Dunbrack ; Anthony Gitter ; 
Kresten Lindorff-Larsen ; Sergey Ovchinnikov ; Polizzi, Nicholas F. 
; Brian Shoichet 
Subject: AlphaFold3 Transparency and Reproducibility


This email from mullane.stepha...@gmail.com originates from outside Imperial. Do 
not click on links and attachments unless you recognise the sender. If you trust the 
sender, add them to your safe senders list 
 to disable email stamping for 
this address.

Hello,


As many of you, we were incredibly disappointed with the lack of code or 
even executables accompanying the publication of AlphaFold3 in Nature. 
AlphaFold3 was released without the means to test and use the software in a 
high-throughput manner. This does not align with the principles of scientific 
research, which rely on the ability of the community to evaluate, use, and 
build upon existing work.



We have written a letter, which will be posted on Zenodo and submitted as a 
Letter to the Editor in the coming days.



Please see the entire letter here. 

 If you want to endorse this letter, please fill out your name, affiliation, and 
email in the form.



Additionally, a PDF version of the letter can be found here 
.



Thank you,



Stephanie Wankowicz, UCSF

Pedro Beltrao, ETH
Benjamin Cravatt, Scripps
Roland Dunbrack, FCCC
Anthony Gitter, UW Madison
Kresten Lindorff-Larsen, Copenhagen
Sergey Ovchinnikov, MIT
Nicholas Polizzi, DFCI/HMS
Brian Shoichet, UCSF
James Fraser, UCSF





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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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--
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
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Universidade Nova de Lisboa
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ITQB NOVA, a great choice for your PhD
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[ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

[Harry Powell]

Hi folks

This arrived in my inbox this morning, and I believe that it may provoke some 
discussion…

Wikipedia tells me: στέργει γὰρ οὐδεὶς ἄγγελον κακῶν ἐπῶν

Best wishes!

Harry

>From: Stephanie Wankowicz  
>Sent: Saturday, May 11, 2024 3:31 PM
>To: James Fraser ; Pedro Beltrao 
> ; Benjamin Cravatt ; Roland 
> Dunbrack ; Anthony Gitter 
> ; Kresten Lindorff-Larsen ; 
> Sergey Ovchinnikov ; Polizzi, Nicholas F. 
> ; Brian Shoichet 
>Subject: AlphaFold3 Transparency and Reproducibility
> 
> 
>This email from mullane.stepha...@gmail.com originates from outside 
> Imperial. Do not click on links and attachments unless you recognise the 
> sender. If you trust the sender, add them to your safe senders list 
>  to disable email stamping 
> for this address. 
> 
>Hello,
> 
> 
>As many of you, we were incredibly disappointed with the lack of code or 
> even executables accompanying the publication of AlphaFold3 in Nature. 
> AlphaFold3 was released without the means to test and use the software in a 
> high-throughput manner. This does not align with the principles of scientific 
> research, which rely on the ability of the community to evaluate, use, and 
> build upon existing work. 
> 
> 
> 
>We have written a letter, which will be posted on Zenodo and submitted as 
> a Letter to the Editor in the coming days.
> 
> 
> 
>Please see the entire letter here. 
> 
>  If you want to endorse this letter, please fill out your name, affiliation, 
> and email in the form. 
> 
> 
> 
>Additionally, a PDF version of the letter can be found here 
> .
>  
> 
> 
> 
>Thank you, 
> 
> 
> 
>Stephanie Wankowicz, UCSF
> 
>Pedro Beltrao, ETH
>Benjamin Cravatt, Scripps
>Roland Dunbrack, FCCC
>Anthony Gitter, UW Madison
>Kresten Lindorff-Larsen, Copenhagen
>Sergey Ovchinnikov, MIT
>Nicholas Polizzi, DFCI/HMS
>Brian Shoichet, UCSF
>James Fraser, UCSF
> 
> 



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[ccp4bb] Fwd: REMINDER -- EMBO practical course (8th-12th July, 2024) on time-resolved serial macromolecular crystallography (TR-SX) at French-Alps

[Shibom Basu]

Dear Everyone!

A quick reminder for the deadline to register to our EMBO course on 
Time-resolved serial macromolecular crystallography! Deadline is in 1 week!


Please hurry up to be a part of this excellent brand new course (details 
given below).


Bests,

shibom

On behalf of *Scientific organizers Team
*

Oskar Aurelius, Gisela Branden, Shibom Basu, Arwen Pearson, and Daniele 
de Sanctis



 Forwarded Message 
Subject: 	REMINDER -- EMBO practical course (8th-12th July, 2024) on 
time-resolved serial macromolecular crystallography (TR-SX) at French-Alpes

Date:   Tue, 2 Apr 2024 20:17:23 +0200
From:   Shibom Basu 
To: CCP4BB@JISCMAIL.AC.UK



Dear Everyone!

This is a quick reminder that deadline for registration for our EMBO 
practical course on TR-SX is approaching in 2 weeks!


Our EMBO practical course on TR-SX will be held at beautiful 
French-Alpine valley of Grenoble, France, from *8*_*th – 12th July, 
2024*_. The course aims to train next generation researchers in the 
field of TR-SX with hands-on training from micro-crystallization, TR-SX 
data collection, processing up to difference electron density map. We 
have a diverse and excellent list of speakers/trainers from the field.


Please take a look at the course webpage: 
https://www.embl.org/about/info/course-and-conference-office/events/ser24-01/


Advanced PhD students, postdocs, or early career researcher in the field 
are highly encouraged to apply and we will select 20 participants based 
on motivational letters/CV. Accommodations and meals are fully covered 
for the participants.


Application deadline: *15th April, 2024.
*

The course will offer plenty of time for discussion and opportunities 
for interactions from all career levels. Distinct events are 
incorporated to help participants for network and further their 
opportunities.


Best,

*Scientific organizers Team
*

Oskar Aurelius, Gisela Branden, Shibom Basu, Arwen Pearson, and Daniele 
de Sanctis


--
Shibom Basu, PhD.
Staff Scientist
European Molecular Biology Laboratory (EMBL)
71 avenue des Martyrs, CS 90181,
38042 Grenoble Cedex 9
France
Ph: +33-(0)-4 76 20 78 75



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[ccp4bb] Fwd: Sixth ESRF-INSTRUCT workshop on sample preparation for cryo-EM, May 28-30, 2024

[David FLOT]

-
Dear all,

Quick reminder that the last date to register for the ESRF-INSTRUCT 
hands-on workshop on sample preparation for cryo-EM is approaching (7th 
April).


The registration link is below.

https://survey.esrf.fr/index.php/849989?newtest=Y=en

and the workshop webpage is

https://www.esrf.fr/home/events/conferences/content/area-events/esrf-events-list/instruct-cryo-em-workshop-1.html

Best regards,

Isai




 Forwarded Message 
Subject: 	[ccpem] Sixth ESRF-INSTRUCT workshop on sample preparation 
for cryo-EM, May 28-30, 2024

Date:   Fri, 15 Mar 2024 08:33:49 +0100
From:   Eaazhisai KANDIAH 
Reply-To:   Eaazhisai KANDIAH 
Organization:   ESRF
To: cc...@jiscmail.ac.uk



Dear colleague,

We are pleased to announce the sixth practical hands-on workshop on 
sample preparation for cryo-EM single particle data collection, 
jointly organized by the ESRF, EMBL Grenoble, and the IBS, continuing 
a series started in 2018. This 2.5 day workshop is aimed at PhDs, 
Postdocs and young scientists new to the field of single particle 
cryo-EM and will be held at the European Photon Neutron campus, 
Grenoble, France from M*ay 28^th to 30^th , 2024*. The course offers 
theoretical and practical aspects of sample preparation for single 
particle cryo-EM including prior quality control by negative staining. 
The participants will also learn the basics of grid screening and 
evaluation.


There is *no registration fee* and meals and accommodation during the 
workshop will be provided free of charge. However, participants should 
arrange and pay for their own travel to/from Grenoble. A maximum of 16 
participants will be selected and we will accept participants’ samples 
to be tested during the workshop, if the samples deemed suitable. In 
the case that you plan to bring your own sample, please clearly 
mention this in your cover letter, also indicating the importance of 
the project.


Application for the workshop is open 
 and the 
*deadline for application is April 7**^th **, 2024*. Successful 
candidates will be informed during the first week after the deadline. 
For more information, please consultINSTRUCT CRYO-EM WORKSHOP 
(esrf.fr) 
. 
For any inquiries, please write to cryo-em202...@esrf.fr


This is an in-person workshop and is co-funded by INSTRUCT (IBS).

Best wishes,

Isai (on behalf of the organising committee)

--

*Dr. Eaazhisai Kandiah*

CM01 beamline

https://www.esrf.fr/CM01

71 Avenue des Martyrs, 38000 Grenoble
Telephone: +33 476 882691
Email: eaazhisai.kand...@esrf.fr 




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[ccp4bb] Fwd: [ccp4bb] mmCIF files from PDB format for AlphaFill

[Nicholas Clark]

Hi Harry,

Unfortunately, I did not see that the latest binary update was from 2008. I
do not have access to any newer binaries for Linux, as I'm on MacOS.

Maybe you can use the MineProt software from the quote I mentioned
previously to (in a roundabout way) accomplish the CIF file generation?

"“Huiwenke:

MineProt (https://github.com/huiwenke/MineProt) can be used to curate
AlphaFold predictions, where PDBs are converted into CIFs using MAXIT (
https://sw-tools.rcsb.org/apps/MAXIT/index.html). The generated CIF files
support Mol* visualization and downstream analysis such as AlphaFill (
https://github.com/PDB-REDO/alphafill).
Another possible option is to use MAXIT directly, while it needs several
additional steps to make generated CIF files support older versions of
Mol*. Please refer to
https://github.com/huiwenke/MineProt/blob/master/web/api/pdb2alphacif/index.php
.”"

Best,

Nick



-- Forwarded message -
From: Nicholas Clark 
Date: Fri, Feb 23, 2024 at 8:03 AM
Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill
To: Harry Powell 
Cc: Harry Powell 


Hi Harry,

MAXIT binaries are located here:

https://sw-tools.rcsb.org/apps/MAXIT/binary.html

Best,

Nick


Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908


On Fri, Feb 23, 2024 at 7:58 AM Harry Powell 
wrote:

> Hi Nick
>
> Thanks for responding, but see my earlier reply to Avinash - the build
> doesn’t like my brand-new, hot off the production line Linux and the
> location of pre-built exes is not obvious.
>
> best wishes
>
> Harry
>
> > On 23 Feb 2024, at 12:43, Nicholas Clark <
> b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Hi Harry,
> >
> > Have you tried MAXIT from the PDB? It can be installed locally:
> >
> >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsw-tools.rcsb.org%2Fapps%2FMAXIT%2Findex.html=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=W3%2BzEKkB1%2BpJznVNIUjTDqMcww3v3YxylxULJCOLgf4%3D=0
> >
> > Best,
> >
> > Nick Clark
> >
> > Nicholas D. Clark (He/Him)
> > PhD Candidate
> > Malkowski Lab
> > University at Buffalo
> > Department of Structural Biology
> > Jacob's School of Medicine & Biomedical Sciences
> > 955 Main Street, RM 5130
> > Buffalo, NY 14203
> >
> > Cell: 716-830-1908
> >
> >
> > On Fri, Feb 23, 2024 at 7:36 AM Harry Powell <
> 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> > Hi Martin, Marcin, Arturo, Avinash
> >
> > First off, I’m **NOT** saying that there’s anything wrong with the CIF
> files produced by these routes - just that AlphaFill doesn’t like them (it
> *does* like CIFs from AlphaFold -
> >
> > > alphafill process alphafold.cif filled.cif
> > > 1DKE
>  =---  14%
> >
> > But (while Alphafold models are wonderful, have put us all out of jobs,
> etc, etc) they are just a starting point for my project and, for this
> purpose, no good in themselves.
> >
> > Martin, Marcin - gemmi would be a good way to go, but -
> >
> > > >>> import gemmi
> > > >>> structure = gemmi.read_structure('old.pdb')
> > > >>> structure.make_mmcif_document().write_file('new.cif')
> > >
> > > alphafill process new.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
> >
> > > gemmi convert old.pdb gemmi.cif
> > > alphafill process gemmi.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
> >
> > :-(
> >
> > Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics
> interface -
> >
> > > alphafill process pymol.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps
> pdbx_poly_seq_scheme is missing?
> >
> >
> > Avinash - Maxit *might* work, but I fell at the first hurdle - although
> the help page says
> >
> > > Note: It is highly recommended to utilize binary distribution,
> >
> > it’s not obvious where to get this. So I download and try to build from
> source, and get (after unpacking and setting ENVs) -
> >
> > > make
> > > Warning: this seems to be an unsupported operating system.
> > >
> > > Supported systems are:
> > >   SunOS .. version 4.1.x and 5.2 or higher
> > >   Linux .. any version
> > >   SGI IRIX ... version 5.3-6.4
> > > make: *** [Makefile:32: compile] Error 1
> >
> > which is odd, because this is a new Linux system installed this week
> >
> > > [hpowell@ld-mjeste3 maxit-v11.100-prod-src]$ more /etc/redhat-release
> > > Rocky Linux release 9.3 (Blue Onyx)
> >
> > best wishes all
> >
> > Harry
> >
> >
> >
> > >
> > > On 23 Feb 2024, at 11:55, Martin Malý  wrote:
> > >
> > 

[ccp4bb] Fwd: postdoc post at world-renowned Astbury Centre, in Leeds, UK

[Ville Uski]

-- Forwarded message -
From: Helen McAllister 
Date: Fri, 16 Feb 2024 at 13:10
Subject: [CCP4] Please could you advertise another post for us?
To: c...@listserv.stfc.ac.uk 


Dear Sirs,



Please could you advertise the following post on your website? (This is by
coincidence the second post in a week, not a duplication.)



*New, exciting interdisciplinary postdoc post at world-renowned Astbury
Centre, in exciting and popular city of Leeds, UK, with Profs Radford and
Ranson, working on outer membrane proteins. Please contact either for more
details.*

*https://jobs.leeds.ac.uk/vacancy.aspx?ref=FBSAS1075
*



Very many thanks indeed!



Best wishes



*Helen*



Helen McAllister (Mrs), h.mcallis...@leeds.ac.uk

PA to Professor Sheena Radford, OBE, FRS, FMedSci

School of Cellular and Molecular Biology, Faculty of Biological Sciences

The University of Leeds, Leeds LS2 9JT

Working at home 4 days, and usually on campus on Fridays

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[ccp4bb] Fwd: Open Position (tenure track) - Scientist in Neutron Spectroscopy - at PSI/LNS

[Schertler Gebhard]

Prof. em. Gebhard F.X. Schertler
Strukturbiologie ETH Zürich

ERC Investigator
Head of Biology and Chemistry
Division
Paul Scherrer Institut
OSRA 007
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265

Anfang der weitergeleiteten Nachricht:

Von: PSI User Office 
Datum: 13. Februar 2024 um 09:24:19 MEZ
An: Schertler Gebhard 
Betreff: Open Position (tenure track) - Scientist in Neutron Spectroscopy - at  
PSI/LNS

There is an open tenure track position for a Scientist in Neutron Spectroscopy 
within the "Solid State Dynamics Group" (Laboratory for Neutron Scattering and 
Imaging, LNS) at the Paul Scherrer Institute, Villigen, Switzerland.

Further information and online application:
https://www.psi.ch/en/pa/job-opportunities/61678-scientist-in-neutron-spectroscopy

Contact:
Dr Christof Niedermayer, email: christof.niederma...@psi.ch, phone: 
+41-56-310-2086

Application deadline:
13 March 2024

Paul Scherrer Insitut, Human Resources Management, Sevil Miniti, 5232 Villigen 
PSI, Switzerland


We apologize for multiple receipt of this posting!


-
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[ccp4bb] Fwd: [CCP4] Postdoc position currently available in Leeds

[Ville Uski]

-- Forwarded message -
From: Helen McAllister 
Date: Tue, 5 Dec 2023 at 11:57
Subject: [CCP4] Postdoc position currently available in Leeds
To: c...@listserv.stfc.ac.uk 


Dear Sirs,



Please would it be possible to advertise the job below to your members for
us? (You may need to shorten it a bit!)


We have a postdoc position currently available in the Radford /  Calabrese
laboratories at Leeds. We are looking for a Research Fellow in Integrative
Structural Molecular Biology, with experience in one or more of the
following: Application of biophysical techniques to the study of protein
structure, protein interactions and/or protein folding, such as CD,
fluorescence, SPR, ITC, X-ray crystallography, cryo-EM; Structural
proteomics methods (e.g. chemical crosslinking, native mass spectrometry,
hydrogen-deuterium exchange); NMR spectroscopy of proteins and their
interactions; and/or Molecular biology, protein expression and
characterisation of protein structure, function and binding.



We have a great group of over 20 postdocs and PhD students in our labs, and
superb facilities here in the Astbury Centre.



Here is the link:

*https://jobs.leeds.ac.uk/vacancy.aspx?ref=FBSAS1072
 *


Many thanks for any help you can give, and best wishes to you all,


*Helen*

Helen McAllister (Mrs), h.mcallis...@leeds.ac.uk
PA to Professor Sheena Radford, OBE, FRS, FMedSci
School of Cellular and Molecular Biology, Faculty of Biological Sciences
The University of Leeds, Leeds LS2 9JT
Working at home 4 days, and usually on campus on Fridays

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[ccp4bb] Fwd: Post-Doctoral Position in Integrative structural biology of sarcomeric cytoskeleton in @EMBL Grenoble

[Kristina Djinovic Carugo]

Dear All,


We are recruiting a highly motivated a highly motivated*Post-Doctoral 
Scientist *to join**our teamat EMBL Grenoble, interested in the 
molecular mechanisms underlying the architecture and assembly of muscle 
sarcomeres, particular Z-discs. We use a multidisciplinary approach to 
tackle complex biological problems by combining complementary structural 
biology techniques, computational modelling, and other biochemical and 
biophysical methods. The main focus of this position will be integrative 
structural studies of reconstituted assemblies.


*Your role***

•Taking up and leading a challenging structural biology project

•Designing and performing experimental procedures

•Analysing and interpreting experimental data

•Taking part in regular group meetings, unit seminars and international 
conferences


•Staying up to date with the literature and the latest methodological 
developments relevant to the project


You will embark on an exciting journey to decipher the structures of 
selected reconstituted complexes and macromolecular condensates using an 
integrative structural biology approach, which encompasses molecular 
biophysics characterisation, combined with small angles X-ray 
scattering, macromolecular crystallography, and cryo-electron 
microscopy/tomography, depending on their size and dynamics. As a team 
member, you will play a crucial role in uncovering the detailed 
biophysical and structural principles that regulate complex assembly. 
Joining collaborative efforts, you will contribute to the generation of 
a 4D multiscale integrative molecular model.


*You have*

 * PhD degree in molecular biology or a related field

·Extensive experience in molecular cloning, expression, and purification 
of protein complexes is essential.


·Prior knowledge of crystallography and/or single-particle electron 
microscopy is needed.


·Track record of writing papers as evidenced by publications or 
submitted manuscripts.


 * Independence and ability to solve problems
 * Good time management and pro-active attitude
 * Excellent communication skills and ability to work in a team

*You might also have*

·Previous experience in complementary structural biology methods (e.g. 
SAXS), molecular and cell biophysics approaches and cell culture will be 
considered an advantage.


·Experience with cryo-electron tomography.

·Experience with working in multidisciplinary research teams.

**

*Why join us*

The European Molecular Biology Laboratory (EMBL) is one of the 
highest-ranked scientific research organisations in the worldaimed to 
explore the secrets of life. The Headquarters Laboratory is located in 
Heidelberg (Germany) and further Units are situated in Grenoble 
(France), Hamburg (Germany), Hinxton (UK), Rome (Italy) and Barcelona 
(Spain).


EMBL Grenoble shares the European Photon and Neutron Science (EPN) 
Campus with the European Synchrotron Radiation Facility (ESRF), the 
/Institut Laue Langevin /(ILL) and the French national /Institut de 
Biologie Structurale /(IBS), whose complementary and integrated 
facilities provide a vibrant environment for structural biologists.



EMBL Grenoble enables access to state-of-the-art structural biology 
technologies with the local EM facility equipped with the T12 screening 
microscope and a 200kV Glacios microscope with Falcon4i/SelectrisX 
detector. Additionally, we have a regular access to five 300kV 
microscopes located locally at ESRF and at EMBL Heidelberg. Other 
facilities include high-performance computing cluster, dedicated GPU 
workstations for data processing and deep learning applications, ESRF 
synchrotron X-ray beamlines, high-field NMR at the IBS as well as 
mammalian and insect cell facilities, biophysical platform, confocal 
microscopy and high-throughput crystallization facilities.


EMBL is an inclusive, equal opportunity employer offering attractive 
conditions and benefits appropriate to an international research 
organisation with a very collegial and family friendly working 
environment. The remuneration package comprises a competitive salary, a 
comprehensive pension scheme, medical, educational and other social 
benefits, as well as financial support for relocation and installation, 
including your family.


*What else you need to know*

We are Europe’s flagship research laboratory for the life sciences – an 
intergovernmental organisation performing scientific research in 
disciplines including molecular biology, physics, chemistry and computer 
science. We are an international, innovative and interdisciplinary 
laboratory with more than 1900 employees from many nations, operating 
across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, 
Hamburg, Grenoble and Rome.


Our mission is to offer vital services in training scientists, students 
and visitors at all levels; to develop new instruments and methods in 
the life sciences and actively engage in technology transfer activities, 
and to integrate European 

Re: [ccp4bb] Fwd: radiation damage and image discard

[Jorge Iulek]

Thanks, Clemens, yet more program/literature to study (and to come)!

Jorge


On 10/31/23 12:41, Clemens Vonrhein wrote:

Dear Jorge,

as Harry mentioned, autoPROC [1] will automatically exclude image
ranges that are significantly worse than the rest (i.e. add mostly
noise). This could be due to radiation damage, badly centred crystals
or anything else. The so-called "fitness parameter" it uses takes
multiplicity and completeness into account when judging if a set of
images should be excluded [2].

Those automatic decisions seem to work very well in our and our users
hands ... as far as we can tell [3]

Cheers

Clemens

[1] https://www.globalphasing.com/autoproc/
[2] a paper describing this in detail is under review atm
[3] like most software developers we tend to get feedback if
 something doesn't work ;-)

On Tue, Oct 31, 2023 at 10:48:54AM -0400, Jorge Iulek wrote:

Hi,

Well, it seems there are already many good indications to study and to 
work
on.
Thanks, Oliver, Kay, Harry and Graeme!
Now, brain and hands on!

Jorge

 Forwarded Message 
...

Dear all,

I have found many fundamental studies on image processing and refinement
indexes concerning the decision on cutting resolution for a dataset, always
meant to get better models, the final objective. Paired refinement has been
a procedure mostly indicated.
I have been searching studies alike concerning, in these days of 
thousands
of collected images and strong x ray beams, the cutting (or truncation) of
the (sequentially due to rotation method) recorded images in a dataset due
to radiation damage. Once again, I understand the idea is to always produce
better models.
On one hand, the more images one uses, the higher the multiplicity, what
(higher multiplicity) leads to better averaged intensity (provided scaling
makes a good job), on the other hand, the more images one uses, lower
intensity (due to the radiation damage) equivalent reflections come into
play for scaling, etc. How to balance this? I have seen a case in which
truncating images with some radiation damage led to worse CC(1/2) and
 (at the same high resolution shell, multiplicities around 12.3 and
then 5.7), but this might not be the general finding. In a word, are there
indicators of the point where to truncate more precisely the images such
that the dataset will lead to a better model? I understand tracing a sharp
borderline might not be trivial, but even a blurred borderline might help,
specially in the moment of image processing.
I find that in 
https://ccp4i2.gitlab.io/rstdocs/tasks/aimless_pipe/scaling_and_merging.html#estimation-of-resolution
there is a suggestion to try refinement with both truncating and not
truncating.
Sure other factors come into play here, like diffraction anisotropy,
crystal internal symmetry, etc., but to start one might consider just the
radiation damage due to exposure to x rays. Yes, further on, it would be
nice the talk evolves to those cases when we see peaks and valleys along the
rotation due to crystal anisotropy, whose average height goes on
diminishing.
Comments and indications to papers and material to study are welcome.
Thanks.
Yours,

Jorge



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Re: [ccp4bb] Fwd: radiation damage and image discard

[Clemens Vonrhein]

Dear Jorge,

as Harry mentioned, autoPROC [1] will automatically exclude image
ranges that are significantly worse than the rest (i.e. add mostly
noise). This could be due to radiation damage, badly centred crystals
or anything else. The so-called "fitness parameter" it uses takes
multiplicity and completeness into account when judging if a set of
images should be excluded [2].

Those automatic decisions seem to work very well in our and our users
hands ... as far as we can tell [3]

Cheers

Clemens

[1] https://www.globalphasing.com/autoproc/
[2] a paper describing this in detail is under review atm
[3] like most software developers we tend to get feedback if
something doesn't work ;-)

On Tue, Oct 31, 2023 at 10:48:54AM -0400, Jorge Iulek wrote:
> Hi,
> 
>   Well, it seems there are already many good indications to study and to 
> work
> on.
>   Thanks, Oliver, Kay, Harry and Graeme!
>   Now, brain and hands on!
> 
> Jorge
> 
>  Forwarded Message 
> ...
> 
> Dear all,
> 
>   I have found many fundamental studies on image processing and refinement
> indexes concerning the decision on cutting resolution for a dataset, always
> meant to get better models, the final objective. Paired refinement has been
> a procedure mostly indicated.
>   I have been searching studies alike concerning, in these days of 
> thousands
> of collected images and strong x ray beams, the cutting (or truncation) of
> the (sequentially due to rotation method) recorded images in a dataset due
> to radiation damage. Once again, I understand the idea is to always produce
> better models.
>   On one hand, the more images one uses, the higher the multiplicity, what
> (higher multiplicity) leads to better averaged intensity (provided scaling
> makes a good job), on the other hand, the more images one uses, lower
> intensity (due to the radiation damage) equivalent reflections come into
> play for scaling, etc. How to balance this? I have seen a case in which
> truncating images with some radiation damage led to worse CC(1/2) and
>  (at the same high resolution shell, multiplicities around 12.3 and
> then 5.7), but this might not be the general finding. In a word, are there
> indicators of the point where to truncate more precisely the images such
> that the dataset will lead to a better model? I understand tracing a sharp
> borderline might not be trivial, but even a blurred borderline might help,
> specially in the moment of image processing.
>   I find that in 
> https://ccp4i2.gitlab.io/rstdocs/tasks/aimless_pipe/scaling_and_merging.html#estimation-of-resolution
> there is a suggestion to try refinement with both truncating and not
> truncating.
>   Sure other factors come into play here, like diffraction anisotropy,
> crystal internal symmetry, etc., but to start one might consider just the
> radiation damage due to exposure to x rays. Yes, further on, it would be
> nice the talk evolves to those cases when we see peaks and valleys along the
> rotation due to crystal anisotropy, whose average height goes on
> diminishing.
>   Comments and indications to papers and material to study are welcome.
> Thanks.
>   Yours,
> 
> Jorge
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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[ccp4bb] Fwd: radiation damage and image discard

[Jorge Iulek]

Hi,

	Well, it seems there are already many good indications to study and to 
work on.

Thanks, Oliver, Kay, Harry and Graeme!
Now, brain and hands on!

Jorge

 Forwarded Message 
...

Dear all,

	I have found many fundamental studies on image processing and 
refinement indexes concerning the decision on cutting resolution for a 
dataset, always meant to get better models, the final objective. Paired 
refinement has been a procedure mostly indicated.
	I have been searching studies alike concerning, in these days of 
thousands of collected images and strong x ray beams, the cutting (or 
truncation) of the (sequentially due to rotation method) recorded images 
in a dataset due to radiation damage. Once again, I understand the idea 
is to always produce better models.
	On one hand, the more images one uses, the higher the multiplicity, 
what (higher multiplicity) leads to better averaged intensity (provided 
scaling makes a good job), on the other hand, the more images one uses, 
lower intensity (due to the radiation damage) equivalent reflections 
come into play for scaling, etc. How to balance this? I have seen a case 
in which truncating images with some radiation damage led to worse 
CC(1/2) and  (at the same high resolution shell, multiplicities 
around 12.3 and then 5.7), but this might not be the general finding. In 
a word, are there indicators of the point where to truncate more 
precisely the images such that the dataset will lead to a better model? 
I understand tracing a sharp borderline might not be trivial, but even a 
blurred borderline might help, specially in the moment of image processing.
	I find that in 
https://ccp4i2.gitlab.io/rstdocs/tasks/aimless_pipe/scaling_and_merging.html#estimation-of-resolution 
there is a suggestion to try refinement with both truncating and not 
truncating.
	Sure other factors come into play here, like diffraction anisotropy, 
crystal internal symmetry, etc., but to start one might consider just 
the radiation damage due to exposure to x rays. Yes, further on, it 
would be nice the talk evolves to those cases when we see peaks and 
valleys along the rotation due to crystal anisotropy, whose average 
height goes on diminishing.
	Comments and indications to papers and material to study are welcome. 
Thanks.

Yours,

Jorge



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[ccp4bb] Fwd: Position open in the HILIFE Instruct-FI cryoEM unit for a research technician - please distribute

[Kajander, Tommi A]

Daer All,

FYI, we have a job opening in CryoEM for research technician in Helsinki.

Best,
Tommi


Tommi Kajander, Ph.D.
Head of Unit, Protein crystallisation
INSTRUCT-HiLIFE
Institute of Biotechnology
University of Helsinki
Viikinkaari 1 (P.O. Box 65)
00014 Helsinki, Finland
p. +358-50-4480991
http://www.helsinki.fi/kajanderlab



From: "Butcher, Sarah" 
mailto:sarah.butc...@helsinki.fi>>
Subject: Position open in the HILIFE Instruct-FI cryoEM unit for a research 
technician - please distribute
Date: 16. June 2023 at 10.58.16 EEST
To: "Lak, Behnam" mailto:behnam@helsinki.fi>>, John 
Dolan mailto:j...@instruct-eric.org>>, 
"finstruct...@helsinki.fi" 
mailto:finstruct...@helsinki.fi>>, 
"tuesday-biophys...@helsinki.fi" 
mailto:tuesday-biophys...@helsinki.fi>>, 
"cryo...@scilifelab.se" 
mailto:cryo...@scilifelab.se>>, 
"michael.elb...@weizmann.ac.il" 
mailto:michael.elb...@weizmann.ac.il>>, 
"sharon.w...@weizmann.ac.il" 
mailto:sharon.w...@weizmann.ac.il>>, Celia Romao 
mailto:cmro...@itqb.unl.pt>>

Dear all,
we have an opening for a laboratory technician in the HILIFE Instruct-FI cryoEM 
unit, University of Helsinki, Finland. Deadline for applications 27.6.23. 
Please advertise further.
 
https://jobs.helsinki.fi/job/Laboratory-technician%2C-cryogenic-electron-microscopy-service/773176102/?feedId=350602_source=CareerSite_UniversityOfHelsinki

 Best regards

Sarah
_
Prof. Sarah Butcher, Ph.D.
Molecular & Integrative Biosciences Research Programme
Faculty of Biological and Environmental Sciences
&
Helsinki Life Science Institute-Institute of Biotechnology
room 2405
P.O. Box 56 (Viikinkaari 9)
FIN-00014 University of Helsinki
Finland
office: +358 2941 59563
cell: +358 50 4155492

https://researchportal.helsinki.fi/en/persons/sarah-butcher
https://blogs.helsinki.fi/butcher/
https://www.helsinki.fi/en/infrastructures/integrated-structural-cell-biology/cryoem
https://www.vibrant-itn.eu/
https://www.itqb.unl.pt/impact







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[ccp4bb] Fwd: Post-doc opportunity in integrative structural biology (Carlomagno Group, University of Birmingham)

[John Kirkpatrick]

Dear All,


Please see the link below for details about a post-doc (Research Fellow) position available in the 
field of integrative structural biology, based in the group of Prof. Teresa Carlomagno at the 
University of Birmingham.


Research Fellow in Integrative Structural Biology, School of Biosciences, University of Birmingham 




Please send any enquiries by email to: t.carloma...@bham.ac.uk

And for more information on the group, please visit our website: carlomagno-group.org 




Apologies for any cross-posting.

Best wishes,

John



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[ccp4bb] Fwd: Crystallographic Computing School

[Harry Powell]

Dear all

Those of you who are travelling to Melbourne for the IUCr Congress and General 
Assembly in August may be interested in this (which finishes in time to get to 
the opening ceremony of the main Congress). 

To get an idea of the content of the workshop, you may wish to look at tetails 
of previous events held by the IUCr Commission for Crystallographic Computing 
which are are available here - 

> https://www.iucr.org/resources/commissions/computing/schools

Harry


> Begin forwarded message:
> 
> From: "Lutz, M.H. (Martin)" 
> Subject: Crystallographic Computing School
> Date: 23 March 2023 at 10:07:01 GMT
> To: "Lutz, M.H. (Martin)" 
> 
> 
> Dear colleagues,
> 
> as programmers and software developers you may be interested in the 
> Crystallographic Computing School. This is a satellite to the IUCr congress 
> and will take place from 19-Aug to 22-Aug-2023 at the Australian synchrotron 
> in Melbourne. We have a list of very interesting topics and great speakers. 
> Registration is now open.
> 
> http://www.cryst.chem.uu.nl/lutz/IUCrSchool2023/ 
> 
> Best wishes,
> Martin
> 
> --
> Martin Lutz
> Structural Biochemistry
> Bijvoet Centre for Biomolecular Research
> Faculty of Science
> Utrecht University
> Universiteitsweg 99
> 3584 CG Utrecht
> The Netherlands
> Tel. [+31] 06-22735980
>  



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Re: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

[Julia Griese]

Oh, I hadn’t thought of trying that, that works!

Obviously it would still be great if this issue was fixed (I guess it’s MacOS 
rather than PyMOL that’s to blame here), but this is a decent workaround.

Thanks!

/Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/

From: CCP4 bulletin board  on behalf of Nicholas Clark 

Reply-To: Nicholas Clark 
Date: Monday, February 6, 2023 at 12:46
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2



-- Forwarded message -
From: Nicholas Clark mailto:ndcla...@buffalo.edu>>
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese mailto:julia.gri...@icm.uu.se>>

Julia,

I have the same issue with PyMOL. After it opens the blank session, if you 
return to the file explorer and try to reopen the file it will open the session 
correctly. Seems what you’re trying to open gets “lost” while loading PyMOL.

Best,

Nick Clark

On Mon, Feb 6, 2023 at 5:38 AM Julia Griese 
mailto:julia.gri...@icm.uu.se>> wrote:
Hi all,

I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my 
computer’s nagging) and am now encountering some issues with Coot and PyMOL. 
The issues persist after updating to version 13.2.

Regarding Coot version 0.9.8.7<http://0.9.8.7>: The rotate/translate zone 
function does not work properly. Everything works when using the slider bars in 
the dialog, and translating with the mouse works, but rotating with the mouse 
does not work. The region to be rotated disappears from view. I can make do 
with the slider bars, but feel that I have much better fine control and it’s 
much faster when using the mouse to rotate. Has anyone else encountered this 
problem and knows of a workaround?
(I’m aware of the workaround for the main window disappearing when you delete 
items.)

Regarding PyMOL version 2.5.4 (had the same issue with 2.4.1): When I try to 
open any kind of file that is set to open in PyMOL by default (pdb or cif 
coordinates, pse), PyMOL opens, but to an empty session. I can only open PyMOL 
files through the File Open dialog, having to navigate through the entire 
folder structure first, which obviously takes much longer. Has anyone else 
encountered this issue and knows how to fix it?


Best,

Julia

--
Dr. Julia Griese
Assistant Professor/Docent
Department of Cell and Molecular Biology
Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

email: julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se>
phone: +46-(0)18-471 4982
http://www.icm.uu.se/structural-biology/griese-lab/<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.icm.uu.se%2Fstructural-biology%2Fgriese-lab%2F=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C20d5eb5f89124f88131408db082e3833%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638112766972241444%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=8bFzv1MlDG9wxZdBaPgnYX%2BkF%2BrK7TKr%2FGivROK3hXE%3D=0>








När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du 
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For 
more information on how this is performed, please read here: 
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--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908
--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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CAUTION: Do not click on links or open attachments u

[ccp4bb] Fwd: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2

[Nicholas Clark]

-- Forwarded message -
From: Nicholas Clark 
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese 


Julia,

I have the same issue with PyMOL. After it opens the blank session, if you
return to the file explorer and try to reopen the file it will open the
session correctly. Seems what you’re trying to open gets “lost” while
loading PyMOL.

Best,

Nick Clark

On Mon, Feb 6, 2023 at 5:38 AM Julia Griese  wrote:

> Hi all,
>
>
>
> I’ve recently upgraded to MacOS Ventura (yes, I regret giving in to my
> computer’s nagging) and am now encountering some issues with Coot and
> PyMOL. The issues persist after updating to version 13.2.
>
>
>
> *Regarding Coot version 0.9.8.7 :* The rotate/translate
> zone function does not work properly. Everything works when using the
> slider bars in the dialog, and translating with the mouse works, but
> rotating with the mouse does not work. The region to be rotated disappears
> from view. I can make do with the slider bars, but feel that I have much
> better fine control and it’s much faster when using the mouse to rotate.
> Has anyone else encountered this problem and knows of a workaround?
>
> (I’m aware of the workaround for the main window disappearing when you
> delete items.)
>
>
>
> *Regarding PyMOL version 2.5.4 *(had the same issue with 2.4.1): When I
> try to open any kind of file that is set to open in PyMOL by default (pdb
> or cif coordinates, pse), PyMOL opens, but to an empty session. I can only
> open PyMOL files through the File Open dialog, having to navigate through
> the entire folder structure first, which obviously takes much longer. Has
> anyone else encountered this issue and knows how to fix it?
>
>
>
>
>
> Best,
>
>
>
> Julia
>
>
>
> --
>
> Dr. Julia Griese
>
> Assistant Professor/Docent
>
> Department of Cell and Molecular Biology
>
> Uppsala University
>
> BMC, Box 596
>
> SE-75124 Uppsala
>
> Sweden
>
>
>
> email: julia.gri...@icm.uu.se
>
> phone: +46-(0)18-471 4982
>
> http://www.icm.uu.se/structural-biology/griese-lab/
> 
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>
> E-mailing Uppsala University means that we will process your personal
> data. For more information on how this is performed, please read here:
> http://www.uu.se/en/about-uu/data-protection-policy
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908
-- 
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908



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[ccp4bb] Fwd: Register for the Antiviral Drug Discovery (AViDD) Open Science Forum virtual meeting Wed 15 Feb 11.00A ET

[Frank von Delft]

Hello all - slightly off-topic, but many BB readers will find the talks 
at this forum of direct or indeed indirect interest.


They will run monthly, for as long as the AViDD awards run (currently 
middle 2025), and will cover topics of antiviral drug discovery and 
development, from early discovery all the way to pre-clinical development.


See you there!
Frank


 Forwarded Message 
Subject: 	Register for the Antiviral Drug Discovery (AViDD) Open Science 
Forum virtual meeting Wed 15 Feb 11.00A ET

Date:   Mon, 30 Jan 2023 15:59:46 +
From:   AViDD Open Science Forum 
Reply-To:   AViDD Open Science Forum 
To: frank.von-de...@diamond.ac.uk



Register for the Antiviral Drug Discovery (AViDD) Open Science Forum 
virtual meeting Wed 15 Feb 11.00A ET The next Antiviral Drug Discovery 
(AViDD) Open Science Forum virtual meeting will be Wed 15 Feb 11.00A ET


View this email in your browser 




 Antiviral Drug Discovery (AViDD) Open Science Forum

*ANNOUNCEMENT*

To view slides and recordings from the last *Antiviral Drug Discovery 
(AViDD) Open Science Forum* 
**on 
18 Jan 2023 follow the links below:


 *

   *Presentation slides* can be viewed on**the**Antiviral Drug
   Discovery (AViDD) Open Science Forum Zenodo Community.
   


 *

   *Talk recordings* can be viewed on the AViDD Open Science Forum
   YouTube Channel.
   


The next *Antiviral Drug Discovery (AViDD) Open Science Forum* virtual 
meeting 
 
will be *Wed 15 Feb 2023 at 8.00A PT / 11.00A ET / 4.00P UK (GMT+1) / 
5.00P Geneva (GMT+2)*.


Registration link 



/Moderator:/*John Chodera* 
(MSKCC 
)


 *

   *Brian Shoichet, UCSF*
   
*(**QBI
   Coronavirus Research Group*
   
*)*:
   /False-positives in anti-viral drug discovery: mechanistic bases and
   rapid counterscreening assays /[30 min, recorded]

 *

   *Jesse Bloom, Fred Hutch*
   
*(**ASAP*
   
*)*:
   /Fitness effects of mutations to SARS-CoV-2 proteins /[30 min, recorded]

*Moderated discussion* [30 min, unrecorded]

For a schedule of upcoming events, recorded talks, more information, and 
open antiviral discovery resources, see *http://openantivirals.org* 
.


/The AViDD Open Science Forum is not an official NIAID activity. There 
is no requirement for staff from AViDD Centers or NIH staff to 
participate in this forum./


Register for the virtual AViDD Open Science Forum event 
 




Twitter icon 
 



Want to change how you receive these emails?
You can update your preferences 
 
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[ccp4bb] RES: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

[Rafael Marques]

Thank you very much, guys. What I wanted actually was a software that gives the 
formal charge looking at different axis of my model instead of particular 
residues. Then, placing the center of my model at coordinates 0,0,0, I would be 
able to see the sum up of charges at +/- x, +/-y and +/-z. I will take a look 
on the sites and in chimera.

Best wishes


Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester

Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"


De: Jon Cooper<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Enviado:quinta-feira, 29 de dezembro de 2022 13:20
Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Assunto: Re: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

Dear Boaz

I think your original answer must have been steganographic ;-0 Maybe white text 
on a white background ;-? Anyway, I can see it below now that I have started 
typing this reply, and advice is excellent.

My answer to Rafael's question would be to look at apbs:

https://www.poissonboltzmann.org/

This gives you a map of the potential. It's a while since I dabbled with it, 
but I remember using it and it was all pretty workable as a standalone program, 
even for an electrostatics non-specialist. You might need to do some scripting 
to sum up charges, etc, though.

Good luck. Jon.C.

Sent from ProtonMail mobile



 Original Message 
On 28 Dec 2022, 15:57, Boaz Shaanan < bshaa...@bgu.ac.il> wrote:


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
-- Forwarded message --
From: בעז שאנן 
Date: Dec 28, 2022 17:13
Subject: Re: [ccp4bb] Calculate charge on protein surface
To: Rafael Marques 
Cc:

Hi
In ucsf-chimera you can "walk" with the cursor on the surface and it'll show 
the actual porential value at each point in the command line. You have to 
enable this option in the surface drawing panel. I've used this option quite 
often. There may be a similar option in chimerax by now.
My 2p.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Dec 28, 2022 17:03, Rafael Marques  wrote:

Hello guys. I hope you are having a great break and still eating the leftovers 
of your Xmas turkey.



I wonder if there is any software that could provide me numbers regarding the 
formal charge of different sides of my structure. Although I can clearly see 
that one face of it is pretty red, I would like to know “how much” red it is.



Best wishes



Rafael Marques da Silva

PhD Student – Structural Biology

University of Leicester



Mestre em Física Biomolecular

Universidade de São Paulo



Bacharel em Ciências Biológicas

Universidade Federal de São Carlos



phone: +55 16 99766-0021



   "A sorte acompanha uma mente bem treinada"







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Re: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

[Jon Cooper]

Dear Boaz

I think your original answer must have been steganographic ;-0 Maybe white text 
on a white background ;-? Anyway, I can see it below now that I have started 
typing this reply, and advice is excellent.

My answer to Rafael's question would be to look at apbs:

https://www.poissonboltzmann.org/

This gives you a map of the potential. It's a while since I dabbled with it, 
but I remember using it and it was all pretty workable as a standalone program, 
even for an electrostatics non-specialist. You might need to do some scripting 
to sum up charges, etc, though.

Good luck. Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 28 Dec 2022, 15:57, Boaz Shaanan wrote:

> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben Gurion University
> Beer Sheva, Israel
> -- Forwarded message --
> From: בעז שאנן 
> Date: Dec 28, 2022 17:13
> Subject: Re: [ccp4bb] Calculate charge on protein surface
> To: Rafael Marques 
> Cc:
>
>> Hi
>> In ucsf-chimera you can "walk" with the cursor on the surface and it'll show 
>> the actual porential value at each point in the command line. You have to 
>> enable this option in the surface drawing panel. I've used this option quite 
>> often. There may be a similar option in chimerax by now.
>> My 2p.
>> Cheers,
>> Boaz
>>
>> Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben Gurion University
>> Beer Sheva, Israel
>>
>> On Dec 28, 2022 17:03, Rafael Marques  wrote:
>>
>> Hello guys. I hope you are having a great break and still eating the 
>> leftovers of your Xmas turkey.
>>
>> I wonder if there is any software that could provide me numbers regarding 
>> the formal charge of different sides of my structure. Although I can clearly 
>> see that one face of it is pretty red, I would like to know “how much” red 
>> it is.
>>
>> Best wishes
>>
>> Rafael Marques da Silva
>>
>> PhD Student – Structural Biology
>>
>> University of Leicester
>>
>> Mestre em Física Biomolecular
>>
>> Universidade de São Paulo
>>
>> Bacharel em Ciências Biológicas
>>
>> Universidade Federal de São Carlos
>>
>> phone: +55 16 99766-0021
>>
>> "A sorte acompanha uma mente bem treinada"
>>
>> 
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> ---
>
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[ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

[Boaz Shaanan]

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
-- Forwarded message --
From: בעז שאנן 
Date: Dec 28, 2022 17:13
Subject: Re: [ccp4bb] Calculate charge on protein surface
To: Rafael Marques 
Cc:

Hi
In ucsf-chimera you can "walk" with the cursor on the surface and it'll show 
the actual porential value at each point in the command line. You have to 
enable this option in the surface drawing panel. I've used this option quite 
often. There may be a similar option in chimerax by now.
My 2p.
Cheers,
Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Dec 28, 2022 17:03, Rafael Marques  wrote:

Hello guys. I hope you are having a great break and still eating the leftovers 
of your Xmas turkey.



I wonder if there is any software that could provide me numbers regarding the 
formal charge of different sides of my structure. Although I can clearly see 
that one face of it is pretty red, I would like to know “how much” red it is.



Best wishes



Rafael Marques da Silva

PhD Student – Structural Biology

University of Leicester



Mestre em Física Biomolecular

Universidade de São Paulo



Bacharel em Ciências Biológicas

Universidade Federal de São Carlos



phone: +55 16 99766-0021



   "A sorte acompanha uma mente bem treinada"







To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




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[ccp4bb] Fwd: Postdoc position in crystallography-driven drug discovery, Yue Lab at Newcastle University

[Wyatt W. Yue]

A reminder of the below postdoc position in crystallography-driven drug
discovery at Newcastle University, with deadline in a week (*Friday 18th
November*)
Best wishes

*Wyatt Yue*

Professor of Structural Biology

Biosciences Institute

Faculty of Medical Sciences

Newcastle University NE2 4HH

Group: www.staff.ncl.ac.uk/yuelab/

Profile: wyattyue.github.io


-- Forwarded message -
From: Wyatt W. Yue 
Date: Tue, 1 Nov 2022 at 18:02
Subject: Postdoc position in crystallography-driven drug discovery, Yue Lab
at Newcastle University
To: , 


Dear all


The Yue lab in Newcastle University is currently advertising one postdoc
position in x-ray crystallography, funded for two years in the first
instance, open to all UK/EU/non-EU/international applicants.



https://jobs.ncl.ac.uk/job/Newcastle-Research-AssistantAssociate/861857001/



You will be a crystallographer working closely with an industry partner
towards small molecule discovery for a rare misfolding disease. You will
carry out crystallography-based fragment screening and biophysical
validation studies to guide compound design for a metabolic enzyme.



You can find out more about our group here:
https://www.staff.ncl.ac.uk/yuelab/



Any informal enquiries you can contact: wyatt@newcastle.ac.uk



Deadline: Friday 18 November 2022. We aim to hold interviews in the week of
28 Nov - 2 Dec 2022.


*Wyatt Yue*

Professor of Structural Biology

Biosciences Institute

Faculty of Medical Sciences

Newcastle University NE2 4HH

Group: www.staff.ncl.ac.uk/yuelab/

Profile: wyattyue.github.io



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[ccp4bb] Fwd: [ccp4bb] Another folding AI

[Carter, Charlie]

Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] Another folding AI
Date: November 5, 2022 at 12:13:04 PM EDT
To: "Nave, Colin (DLSLtd,RAL,LSCI)" 
mailto:colin.n...@diamond.ac.uk>>

As notable a scientist as Maxwell was, he also has been hailed as a creation 
scientist:  https://creation.com/great-creation-scientists-james-clerk-maxwell

AI approaches to folding are, I’ve found, remarkably accurate surrogates for 
all the many unsolved protein structures. I expect that quite solid research 
projects will eventually emerge that were not possible without the broadened 
database afforded by AF2.

On Nov 5, 2022, at 11:58 AM, Nave, Colin (DLSLtd,RAL,LSCI) 
<64fdcfc6624b-dmarc-requ...@jiscmail.ac.uk>
 wrote:

You don't often get email from 
64fdcfc6624b-dmarc-requ...@jiscmail.ac.uk.
 Learn why this is important
There is another quote from an equally revered physicist – James Clark Maxwell

“The actual science of logic is conversant at present only with things either 
certain, impossible, or entirely doubtful, none of which (fortunately) we have 
to reason on. Therefore the true logic for this world is the calculus of 
Probabilities, which takes account of the magnitude of the probability which 
is, or ought to be, in a reasonable man's mind.”

I will leave people to decide for themselves which of these quotes is most 
relevant to the various AI approaches to protein folding, other than to say 
that at least one of them covers the uncertainty in any structure predictions.

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Bryan Lepore
Sent: 03 November 2022 12:22
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Another folding AI

[ emphasis/bold font is mine]:

“In general we look for a new law by the following process. First we guess it. 
Then we compute the consequences of the guess to see what would be implied if 
this law that we guessed is right. Then we compare the result of the 
computation to nature, with experiment or experience, compare it directly with 
observation, to see if it works. If it disagrees with experiment it is wrong. 
In that simple statement is the key to science. It does not make any difference 
how beautiful your guess is. It does not make any difference how smart you are, 
who made the guess, or what his name is – if it disagrees with experiment it is 
wrong. That is all there is to it.”

-Richard Feynman

The Character of Physical Law (1965)
Chapter 7, “Seeking New Laws”, p.150 (Modern Library edition, 1994)
ISBN 0-679-60127-9



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[ccp4bb] Fwd: Postdoctoral Fellow position at University of Texas Health Science Center San Antonio

[Yogesh Gupta]

My research group at UT Health San Antonio
 is looking for a creative and
self-motivated Postdoctoral Fellow to study the structures and mechanisms
of nucleic acid enzymes. We will use X-ray crystallography, cryoEM, and
enzyme biochemistry to address basic mechanistic questions and develop drug
candidates.


Below are some of our recent publications:
*eLife. *2022 Jan 21;11. PMID: 35060905. doi.org/10.7554/eLife.67150
*Nature Communications*. 2021 Jun 2; 12: 3287. PMID: 34078893. doi:
10.1038/s41467-021-23594-y

*Nature Communications*. 2020 Jul 24;11(1):3718. PMID: 32709886. doi:
10.1038/s41467-020-17496-8




Applicants with prior experience in macromolecular crystallography and a
strong interest in cryoEM studies and drug discovery are encouraged to
apply. We already have crystals and cryoEM datasets available for an
immediate start.


The Greehey Children’s Cancer Research Institute (GCCRI) is a unique,
specialized cancer research center focusing on basic and translational
research in childhood cancer and occupies a state-of-the-art 100,000 sq.
foot research facility on the university’s Greehey Academic and Research
Campus. The GCCRI has significant external funding, a large endowment from
the state, and links to philanthropic entities. San Antonio is the nation’s
seventh-largest city and is located at the edge of the beautiful Texas Hill
County. San Antonio offers a rich, multi-cultural community, affordable
cost of living, excellent weather, and a thriving biomedical industry.


Interested candidates can submit their application (CV, a brief description
of their accomplishments, and contacts of 3 references) directly by email
to me (Email: gup...@uthscsa.edu)

Yogesh

Yogesh Gupta, PhD
Associate Professor of Biochemistry & Structural Biology
Greehey Children's Cancer Research Institute
University of Texas Health Science Center San Antonio
8403 Floyd Curl Drive, San Antonio, TX, USA 78229
Email: gup...@uthscsa.edu
http://ccri.uthscsa.edu/YGupta.html



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[ccp4bb] Fwd: Reminder: CryoEM Centers Webinar Series starts in 1 day

[John Hasty]

This presentation might help.
The live webinar is over but you might find the recorded version sometime time 
later. Good luck
John


Begin forwarded message:

> From: Zoom 
> Date: July 20, 2022 at 6:13:22 AM HST
> To: "j.hasty" 
> Subject: Reminder: CryoEM Centers Webinar Series starts in 1 day
> Reply-To: czima...@nysbc.org
> 
> 
> Hi John, 
> 
> This is a reminder that "CryoEM Current Practices Webinar: Strategies and 
> Highlights from the National CryoEM Centers" will begin in 1 day on:
> Date Time: Jul 21, 2022 12:00 PM Eastern Time (US and Canada) 
> 
> Join from a PC, Mac, iPad, iPhone or Android device: 
> Click Here to Join 
> Note: This link should not be shared with others; it is unique to you.
> Passcode: 019012
> Add to Calendar   Add to Google Calendar   Add to Yahoo Calendar
> 
> Or join by phone:
> 
> US: +1 301 715 8592 or +1 312 626 6799 or +1 346 248 7799 or +1 386 347 5053 
> or +1 564 217 2000 or +1 646 558 8656 or +1 646 931 3860 or +1 669 444 9171 
> or +1 669 900 9128 or +1 253 215 8782 
> Webinar ID: 891 3976 6049 
> Passcode: 019012
> International numbers available: https://us02web.zoom.us/u/kn061qKOS
> 
> 
> 
> 
> You can cancel your registration at any time.
> 
>



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[ccp4bb] Fwd: job opening: Scientist, X-ray Crystallography - San Diego, CA

[Rui Xu]

*Scientist, X-ray Crystallography - San Diego, CA*

Pharmaceuticals

*Job Description *

Janssen Research & Development, L.L.C., a division of Johnson & Johnson's
Family of Companies is recruiting for a Scientist, X-ray Crystallography,
located in La Jolla, CA!

At the Janssen Pharmaceutical Companies of Johnson & Johnson, we are
working to create a world without disease. Transforming lives by finding
new and better ways to prevent, intercept, treat and cure disease inspires
us. We bring together the best minds and pursue the most promising science.
We are Janssen. We collaborate with the world for the health of everyone in
it. Learn more at www.janssen.com and follow us @JanssenGlobal. Janssen
Research & Development, LLC is part of the Janssen Pharmaceutical
Companies.

The Discovery Technologies and Molecular Pharmacology group is a dynamic,
diverse and critical part of the Discovery Sciences organization in Janssen
R We are committed to the discovery and characterization of high-quality
chemical leads needed for the generation of small molecule clinical
compounds in all five Janssen Therapeutic Areas. This mission requires deep
scientific expertise across broad subject areas including chemistry,
cellular and molecular pharmacology, enzymology, screening, protein
science, and structural biology coupled with an ability to work
collaboratively with internal and external partners. Building on a strong
legacy of success, we are currently seeking an outstanding and motivated
individual to join our team as Scientist, X-ray Crystallography.

*As the Scientist you will:*

   - Be an active member of drug discovery teams, working closely with
   computational and medicinal chemists on structure-based drug design
   approaches for small molecule agent optimization.
   - Be responsible for crystallization of protein-small molecule
   complexes, determination of high-resolution structures by X-ray
   crystallography and communicating these results to the project team.
   - Work closely with protein scientists, biophysicists, protein NMR and
   cryo-EM scientists as part of an integrated structural biology effort.
   - Contribute to multidisciplinary Fragment-Based Lead Discovery (FBLD)
   efforts.
   - Contribute to enhance the structural biology scientific expertise of
   the group by publishing high-impact research papers, and presenting at
   scientific conferences, internalizing impactful technologies and platforms,
   and establishing academic collaborations.
   - Mentor lab scientists and contribute to the strategic planning of the
   Structural Biology group.


*Qualifications*

   - BS degree with at least 12 years of experience, OR MS degree with at
   least 9 years of experience, OR a Ph.D. or equivalent and postdoctoral
   experience in structural biology (X-ray crystallography, biophysics,
   protein engineering) or related field is required
   - Expertise with crystallography software packages
   (Phenix/CCP4/PyMol/Moe) in a mixed Linux/Windows computational environment
   is required
   - Scientific expertise in structural biology, with strong experience in
   both protein crystallization and structure determination is required
   - Strong record of external publications and presentations is required
   - Outstanding written and oral communication skills are required
   - Experience in Structure-Guided Drug Design utilizing X-ray
   crystallography is preferred
   - Research experience in cryo-electron microscopy (Cryo-EM),
   Micro-electron diffraction (Micro-ED), protein NMR or orthogonal structural
   biology technologies is preferred
   - Research experience with other biophysical techniques such as MST,
   ITC, NMR, DSF, SPR is preferred
   - Broad knowledge of biophysics, biochemistry, molecular pharmacology,
   and protein sciences is preferred.
   - Experience in scientific programming (Unix shells, Python) is preferred
   - Expertise in one or more of the following therapeutic areas: Oncology,
   Inflammation, Neuroscience, Cardiovascular, and Infectious Diseases is
   preferred

Johnson & Johnson is an Affirmative Action and Equal Opportunity Employer.
All qualified applicants will receive consideration for employment without
regard to race, color, religion, sex, sexual orientation, gender identity,
age, national origin, or protected veteran status and will not be
discriminated against on the basis of disability.


*Primary Location*
United States-California-San Diego-
*Organization*
Janssen Research & Development, LLC (6084)
*Job Function*
R
*Requisition ID*
2005866689W



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Re: [ccp4bb] Fwd: ACA2022: Travel Grant Application Deadline March 31, 2022

[yg60]

This may be a good one for you as well. And they have travel award due mar 31.

Yang

> On Mar 16, 2022, at 4:04 PM, Anna Gardberg  wrote:
> 
> There is a travel award opportunity for students and postdocs to attend ACA 
> 2022 in Portland, Oregon, July 29 - August 2, 2022. I encourage you to apply! 
> The application deadline closes in two weeks. 
> 
> -Anna S. Gardberg, PhD
> ACA Meeting Committee
> Odyssey Pharmaceuticals
> 
> -- Forwarded message -
> From: American Crystallographic Association  >
> Date: Mon, Mar 14, 2022 at 1:11 PM
> Subject: ACA2022: Travel Grant Application Deadline March 31, 2022
> To: mailto:anna.s.gardb...@gmail.com>>
> 
> 
>   
> 
> Travel Grant Application Deadline: 
> March 31, 2022
> The ACA recognizes that presenting research at a conference is an important 
> aspect of a young scientists’ educational and professional development.
> 
>  
> To ensure student and young scientist participation at annual meetings, the 
> ACA provides travel grants to students and postdocs who might not otherwise 
> be able to attend the conference.
> 
>  
> Those interested must apply and be accepted. Funds are to help offset travel 
> and travel-related expenses and range from $599 to $1,200 USD.  
> 
>  
> Find out more about the ACA travel grant program 
> 
>  and, if you are a student, graduate student or postdoc and want to attend 
> ACA2022, apply today!  
> 
>  
> If you are a teacher or advisor please feel free to share this announcement 
> with anyone that may be interested in attending ACA2022!
> 
> Submit a Travel Grant Application
>  
> 
>  
> ACA2022
> 
> Portland, Oregon
> 
> July 29 - August 2, 2022
> 
> www.acameeting.com 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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[ccp4bb] Fwd: ACA2022: Travel Grant Application Deadline March 31, 2022

[Anna Gardberg]

There is a travel award opportunity for students and postdocs to attend ACA
2022 in Portland, Oregon, July 29 - August 2, 2022. I encourage you to
apply! The application deadline closes in two weeks.

-Anna S. Gardberg, PhD
ACA Meeting Committee
Odyssey Pharmaceuticals

-- Forwarded message -
From: American Crystallographic Association 
Date: Mon, Mar 14, 2022 at 1:11 PM
Subject: ACA2022: Travel Grant Application Deadline March 31, 2022
To: 




*Travel Grant Application Deadline: March 31, 2022*

The ACA recognizes that presenting research at a conference is an important
aspect of a young scientists’ educational and professional development.



*To ensure student and young scientist participation at annual meetings,
the ACA provides travel grants to students and postdocs who might not
otherwise be able to attend the conference. *



Those interested must apply and be accepted. Funds are to help offset
travel and travel-related expenses and *range from $599 to $1,200 USD.  *



*Find out more about the ACA travel grant program

and, if you are a student, graduate student or postdoc and want to attend
ACA2022, apply today!  *



If you are a teacher or advisor please feel free to share this announcement
with anyone that may be interested in attending ACA2022!
Submit a Travel Grant Application



*ACA2022*

*Portland, Oregon*

*July 29 - August 2, 2022*

www.acameeting.com

--



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[ccp4bb] Fwd: Postdoctoral Research Associate in Chemical Biology at YSBL

[Mahima Sharma]

Dear colleagues

We have the following position available in the Davies Group at York
Structural Biology Laboratory, UK:
https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885_web_page_id=468064



Applications are invited for either a Research Fellow or a Postdoctoral
Researcher to work on the activity-based proteomics and structural
enzymology of plant polysaccharide-degrading enzyme systems. The work is
funded by an ERC-Synergy grant to York, Barcelona and Leiden and is
available for up to 36 months. You will be supervised by Professor Gideon
Davies  and
will work in the ERC-Synergy team in the York Structural Biology
Laboratory, within Chemistry.

You will conduct research into activity-based probes, and other chemical
biology methods, applied to polysaccharide degrading/modifying enzymes. The
goal is to apply activity-based proteomics methods, in collaboration with
Leiden and Barcelona, to identify key enzyme systems involved in
polysaccharide degradation both fundamentally and for potential
biotechnological exploitation.

Note this post is available at grade 6 or grade with the grade 7 position
demanding a higher degree of experience and leadership. Please only apply
for the position commensurate with your experience and make clear on your
application which grade you are applying for.

*Apply by: 21/01/2022*

*Interview date: TBC*

*For informal enquiries:* please contact Prof Gideon Davies on
gideon.dav...@york.ac.uk

The Department of Chemistry  is one of
the largest and most successful departments at York and we are renowned
internationally for our research. As a department, we strive to provide a
working environment that allows all staff and students to contribute fully,
to flourish, and to excel. We are proud of our Athena SWAN Gold Award
.



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Re: [ccp4bb] [EXTERNAL] [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

[Reza Khayat]

​Dear all,


Thank you for the responses. My question regarding validation was not directed 
at weather the prediction was correct (i.e. sufficiently comparable to the 
experimentally determined structure). I realize this question in itself is not 
easily answered. I also agree with what everyone has written below. My question 
was regarding the geometry of the structure. I also understand that outstanding 
geometry does not indicate an accurately predicted structure -the helix example 
indicated by Tristian. Nonetheless, the server links sent earlier are extremely 
helpful.


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031

From: CCP4 bulletin board  on behalf of F.Xavier 
Gomis-Rüth 
Sent: Tuesday, December 21, 2021 5:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

Dear all,
this is by far not the general case in our hands. Depending on which AlphaFold 
protocol is used, the resulting models have locally disfavourable
geometries–including clashes–, impossible chain crossovers, etc. I would 
definitively recommend everybody to go through the model in detail and perform
a final geometry minimization with Coot and/or Phenix/Refmac. And in these 
cases, general geometry validation as provided by MolProbity
provides a final proof of the computational model.
Best,
Xavier


 Forwarded Message 
Subject:Re: [ccp4bb] Validation of structure prediction
Date:   Tue, 21 Dec 2021 09:43:37 +
From:   Vollmar, Melanie (DLSLtd,RAL,LSCI) 
<64fe7ccc6b4d-dmarc-requ...@jiscmail.ac.uk><mailto:64fe7ccc6b4d-dmarc-requ...@jiscmail.ac.uk>
Reply-To:   Vollmar, Melanie (DLSLtd,RAL,LSCI) 
<mailto:melanie.voll...@diamond.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>


Tristan is spot on. All the predicted structures have near perfect geometry, so 
commonly used validation tools like MolProbity can no longer be applied.

What you need to consider is biological relevance of the predicted model. Does 
the model correctly reflect residue arrangement in the active site? Are domains 
in correct relative orientation to allow for interactions and movements, 
perhaps found by some other assay? Is there appropriate room to fit a 
ligand/cofactor? Are transmembrane helices, if there are any, correctly found?

You need to map the knowledge you have of your protein to the structure and see 
if the atom positions and what you know support each other.

Cheers

M

From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> 
on behalf of Tristan Croll <mailto:ti...@cam.ac.uk>
Sent: 21 December 2021 08:28
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Validation of structure prediction

I agree with Dale. Tools like MolProbity are not the right approach to 
validating a structure prediction. To understand why, just consider that all 
you need to do to get a perfect MolProbity score is predict every structure as 
a single long alpha helix with ideal rotamers, with a kink at each proline.

To validate a predicted structure will require a completely different toolset - 
one that I’m not sure fully exists yet.

— Tristan

> On 20 Dec 2021, at 18:47, Dale Tronrud 
> <mailto:de...@daletronrud.com> wrote:
>
>   I don't see any reason to believe that software designed to validate 
> crystallographic or NMR models would have any utility validating AlphaFold 
> predicted models.  Doesn't the prediction software already ensure that all 
> the indicators used by Molprobity are obeyed?  I'm afraid that the tools to 
> validate any new technique must be designed specifically for that technique. 
> (And when they become available they will be useless for validating 
> crystallographic models!)
>
> Dale E. Tronrud
>
>> On 12/20/2021 10:28 AM, Nicholas Clark wrote:
>> The Molprobity server can be run online and only requires the coordinates in 
>> PDB format: 
>> http://molprobity.biochem.duke.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__molprobity.biochem.duke.edu_=DwMDaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=Ore7pZl_g57-Bha3m6bv3ayt12QpXPz1lbBlJYIx0rY=ekPRcBIEvpMpSOCQ3Iwa3WeIz5hew6AEXPmRUbWF9eg=>
>>  
>> <http://molprobity.biochem.duke.edu/<https://urldefense.proofpoint.com/v2/url?u=http-3A__molprobity.biochem.duke.edu_=DwMDaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=Ore7pZl_g57-Bha3m6bv3ayt12QpXPz1lbBlJYIx0rY=ekPRcBIEvpMpSOCQ3Iwa3WeIz5hew6AEXPmRUbWF9eg=>>.
>> Best,
>> Nick Clark
>> On Mon, Dec 20, 2021 at 11:10 AM Reza Khayat 
>> mailto:rkha...@ccny.cuny.edu> 
>

Re: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

[Vollmar, Melanie (DLSLtd,RAL,LSCI)]

I also should have added that if you use a predicted structure and you run MR 
with it and then modify it to fit the data of your novel structure then, for 
sure, MolProbity applies or other tools as you will find in the various 
packages and on the PDB site.

The most current predicted structures usually do have an energy minimisation 
step at the end but nevertheless you can always add it yourself as Xavier 
pointed out.

In general, your prediction is a very good, educated guess on what your protein 
might look like. However,  the algorithm has no clue about your crystallisation 
condition or even the true biological environment in the cell and hence cannot 
take this chemical information into account when arranging the atoms. The 
algorithm also doesn't know that you have a membrane protein or different 
domains that need to be arranged relative to each other. The artefacts 
mentioned by Xavier are most likely a result for this lack of knowledge by the 
algorithm. Or just poor performance after all, even the best predictor can't do 
magic...

Look at the pLDDT score for your prediction, a local measure for the confidence 
with which each residue was placed into 3D space. A low score (<50) means high 
uncertainty and these residues should be removed anyway.

So, open your model in Coot, look at it and remove the rubbish...

M

From: CCP4 bulletin board  on behalf of F.Xavier 
Gomis-Rüth 
Sent: 21 December 2021 10:04
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

Dear all,
this is by far not the general case in our hands. Depending on which AlphaFold 
protocol is used, the resulting models have locally disfavourable
geometries–including clashes–, impossible chain crossovers, etc. I would 
definitively recommend everybody to go through the model in detail and perform
a final geometry minimization with Coot and/or Phenix/Refmac. And in these 
cases, general geometry validation as provided by MolProbity
provides a final proof of the computational model.
Best,
Xavier


 Forwarded Message 
Subject:Re: [ccp4bb] Validation of structure prediction
Date:   Tue, 21 Dec 2021 09:43:37 +
From:   Vollmar, Melanie (DLSLtd,RAL,LSCI) 
<64fe7ccc6b4d-dmarc-requ...@jiscmail.ac.uk><mailto:64fe7ccc6b4d-dmarc-requ...@jiscmail.ac.uk>
Reply-To:   Vollmar, Melanie (DLSLtd,RAL,LSCI) 
<mailto:melanie.voll...@diamond.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>


Tristan is spot on. All the predicted structures have near perfect geometry, so 
commonly used validation tools like MolProbity can no longer be applied.

What you need to consider is biological relevance of the predicted model. Does 
the model correctly reflect residue arrangement in the active site? Are domains 
in correct relative orientation to allow for interactions and movements, 
perhaps found by some other assay? Is there appropriate room to fit a 
ligand/cofactor? Are transmembrane helices, if there are any, correctly found?

You need to map the knowledge you have of your protein to the structure and see 
if the atom positions and what you know support each other.

Cheers

M

From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> 
on behalf of Tristan Croll <mailto:ti...@cam.ac.uk>
Sent: 21 December 2021 08:28
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Validation of structure prediction

I agree with Dale. Tools like MolProbity are not the right approach to 
validating a structure prediction. To understand why, just consider that all 
you need to do to get a perfect MolProbity score is predict every structure as 
a single long alpha helix with ideal rotamers, with a kink at each proline.

To validate a predicted structure will require a completely different toolset - 
one that I’m not sure fully exists yet.

— Tristan

> On 20 Dec 2021, at 18:47, Dale Tronrud 
> <mailto:de...@daletronrud.com> wrote:
>
>   I don't see any reason to believe that software designed to validate 
> crystallographic or NMR models would have any utility validating AlphaFold 
> predicted models.  Doesn't the prediction software already ensure that all 
> the indicators used by Molprobity are obeyed?  I'm afraid that the tools to 
> validate any new technique must be designed specifically for that technique. 
> (And when they become available they will be useless for validating 
> crystallographic models!)
>
> Dale E. Tronrud
>
>> On 12/20/2021 10:28 AM, Nicholas Clark wrote:
>> The Molprobity server can be run online and only requires the coordinates in 
>> PDB format: http://molprobity.biochem.duke.edu/ 
>> <http://molprobity.biochem.duke.edu/>.
>> Best,
>> Nick Clark
>> On Mon, Dec 20, 2021 at 11:10

[ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

[F . Xavier Gomis-Rüth]

Dear all,
this is by far not the general case in our hands. Depending on which 
AlphaFold protocol is used, the resulting models have locally disfavourable
geometries–including clashes–, impossible chain crossovers, etc. I would 
definitively recommend everybody to go through the model in detail and 
perform
a final geometry minimization with Coot and/or Phenix/Refmac. And in 
these cases, general geometry validation as provided by MolProbity

provides a final proof of the computational model.
Best,
Xavier


 Forwarded Message 
Subject:Re: [ccp4bb] Validation of structure prediction
Date:   Tue, 21 Dec 2021 09:43:37 +
From: 	Vollmar, Melanie (DLSLtd,RAL,LSCI) 
<64fe7ccc6b4d-dmarc-requ...@jiscmail.ac.uk>
Reply-To: 	Vollmar, Melanie (DLSLtd,RAL,LSCI) 


To: CCP4BB@JISCMAIL.AC.UK



Tristan is spot on. All the predicted structures have near perfect 
geometry, so commonly used validation tools like MolProbity can no 
longer be applied.


What you need to consider is biological relevance of the predicted 
model. Does the model correctly reflect residue arrangement in the 
active site? Are domains in correct relative orientation to allow for 
interactions and movements, perhaps found by some other assay? Is there 
appropriate room to fit a ligand/cofactor? Are transmembrane helices, if 
there are any, correctly found?


You need to map the knowledge you have of your protein to the structure 
and see if the atom positions and what you know support each other.


Cheers

M

*From:* CCP4 bulletin board  on behalf of Tristan 
Croll 

*Sent:* 21 December 2021 08:28
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] Validation of structure prediction
I agree with Dale. Tools like MolProbity are not the right approach to 
validating a structure prediction. To understand why, just consider that 
all you need to do to get a perfect MolProbity score is predict every 
structure as a single long alpha helix with ideal rotamers, with a kink 
at each proline.


To validate a predicted structure will require a completely different 
toolset - one that I’m not sure fully exists yet.


— Tristan

> On 20 Dec 2021, at 18:47, Dale Tronrud  wrote:
>
>   I don't see any reason to believe that software designed to 
validate crystallographic or NMR models would have any utility 
validating AlphaFold predicted models. Doesn't the prediction software 
already ensure that all the indicators used by Molprobity are obeyed?  
I'm afraid that the tools to validate any new technique must be designed 
specifically for that technique. (And when they become available they 
will be useless for validating crystallographic models!)

>
> Dale E. Tronrud
>
>> On 12/20/2021 10:28 AM, Nicholas Clark wrote:
>> The Molprobity server can be run online and only requires the 
coordinates in PDB format: http://molprobity.biochem.duke.edu/ 
.

>> Best,
>> Nick Clark
>> On Mon, Dec 20, 2021 at 11:10 AM Reza Khayat >> wrote:

>>    ​Hi,
>>    Can anyone suggest how to validate a predicted structure? Something
>>    similar to wwPDB validation without the need for refinement
>>    statistics. I realize this is a strange question given that the
>>    geometry of the model is anticipated to be fine if the structure was
>>    predicted by a server that minimizes the geometry to improve its
>>    statistics. Nonetheless, the journal has asked me for such a report.
>>    Thanks.
>>    Best wishes,
>>    Reza
>>    Reza Khayat, PhD
>>    Associate Professor
>>    City College of New York
>>    Department of Chemistry and Biochemistry
>>    New York, NY 10031
>> 
>>    To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 

>>    >

>> --
>> Nicholas D. Clark
>> PhD Candidate
>> Malkowski Lab
>> University at Buffalo
>> Department of Structural Biology
>> Jacob's School of Medicine & Biomedical Sciences
>> 955 Main Street, RM 5130
>> Buffalo, NY 14203
>> Cell: 716-830-1908
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
 
>

>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> 

[ccp4bb] Fwd: [ccpem] Tenure track scientist position at PSI (focus on cryo-ET)

[Schertler Gebhard (PSI)]

Prof. Gebhard F.X. Schertler
Structural Biology ETH Zürich D-BIOL

Head of Biology and Chemistry
Division
Paul Scherrer Institut
Laboratory of Biomolecular Research,
LBR
OSRA 007
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265

Anfang der weitergeleiteten Nachricht:

Von: "Korkhov Volodymyr (PSI)" 
Datum: 12. Dezember 2021 um 09:38:42 MEZ
An: cc...@jiscmail.ac.uk
Betreff: Aw: [ccpem] Tenure track scientist position at PSI (focus on cryo-ET)
Antwort an: "Korkhov Volodymyr (PSI)" 

Dear all,

This is a gentle reminder that the deadline for the tenure-track cryo-EM 
scientist position at PSI is coming up in 3 days (15th of December).

Best,
Vladimir


On 12 Nov 2021, at 15:25, Vladimir Korkhov  wrote:

The group of Volodymyr Korkhov at Paul Scherrer Institute, Villigen, 
Switzerland is looking to fill a position of a Scientist (Tenure Track), with a 
focus on cryo-electron tomography. The scientist will use cryo-electron 
tomography and single particle analysis to study the structure and organisation 
of membrane protein complexes involved in cellular signalling.

Your tasks:
- Leading new research projects on cryo-EM structure determination of membrane 
proteins within the Mechanisms of signal transduction group, including 
collaborations
- Support of ongoing research projects, including training of PhD students and 
postdocs
- Implementation and development of advanced data collection and image 
processing methods, including cryo-ET & sub-tomogram averaging and single 
particle analysis

Your profile:
- PhD degree in a life science-related discipline
- Strong background on cryo-ET and/or single particle analysis data collection 
and processing
- Capable of performing the full range of cryo-EM workflows, from sample 
preparation to data interpretation
- Interested in membrane biology
- Expertise in data science / programming, FIB-SEM, cell biology or 
biochemistry will be an advantage
- Your are a highly motivated person and able to work in an international team
- It is expected that your are a communicative person, innovative and 
open-minded for new ideas

We offer:
- Access to the EM facility at PSI and to ScopeM at ETH Zurich (equipped with a 
wide range of state of the art equipment, including three Titan Krios 
microscopes)
- Access to all shared research infrastructure and research platforms at PSI 
and at ETH Zurich

Our institution is based on an interdisciplinary, innovative and dynamic 
collaboration. You will profit from a systematic training on the job, in 
addition to personal development possibilities and our pronounced vocational 
training culture. If you wish to optimally combine work and family life or 
other personal interests, we are able to support you with our modern employment 
conditions and the on-site infrastructure.

This is a Tenure Track position. The employment contract will initially be 
limited to 3 years.

For further information, please contact Prof Dr. Volodymyr Korkhov, phone +41 
56 310 28 42, e-mail: volodymyr.kork...@psi.ch.

Please submit your application online by 15 December 2021 (including list of 
publications and addresses of referees) for the position as a Scientist (Tenure 
Track) (index no. 2318-01).

The full job advertisement can be found here:
https://www.nature.com/naturecareers/job/scientist-tenure-track-focus-on-cryoelectron-tomography-paul-scherrer-institute-psi-749597



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[ccp4bb] Fwd: 3 postdoc positions on structure-based drug discovery in the Yue lab at Newcastle University

[Wyatt W. Yue]

A reminder of the below 3 postdoc openings in the Yue lab at Newcastle
University
7 more days to apply
Deadline Monday 13 December

-- Forwarded message -
From: Wyatt W. Yue 
Date: Mon, 29 Nov 2021 at 11:10
Subject: 3 postdoc positions on structure-based drug discovery in the Yue
lab at Newcastle University
To: , 

Dear all,

The Yue Lab, recently relocated to Newcastle, is recruiting 3 postdoc
positions offering exciting opportunities in different flavours of
structural biology/drug discovery, interacting closely with clinicians,
industry, and patient groups.

All are two-year positions in the first instance,
UK/EU/non-EU/international applicants all welcome.

Deadline: *Monday 13 December*. We aim to fill these positions by Q1 2022.

https://jobs.ncl.ac.uk/job/Newcastle-Research-Associate/711931801/ (job ID:
11461) You will drive a structure-based drug discovery project in an
academic setting, funded by LifeArc and Action Medical Research, working
closely with medicinal chemists in Oxford and clinical scientists in UCL
towards hit-to-lead inhibitor optimisation for a rare epileptic disorder.
(Skills: crystallography, SPR, activity assays, CETSA; bit of cryo-EM)

https://jobs.ncl.ac.uk/job/Newcastle-Research-Associate-in-Structure-Based-Drug-Design/711711601/
(job ID: 11462) You will run an academic-industrial collaboration with
Bicycle Therapeutics, towards structural and biophysical characterisation
of bicyclic peptides in complex with novel therapeutic targets in
immune-metabolism/oncology. (Skills: different expression approaches,
crystallography, SPR; bit of cryo-EM)

https://jobs.ncl.ac.uk/job/Newcastle-Research-AssistantAssociate-in-AI-&-fragment-based-drug-discovery/743752301/
(job ID: 13927) You will lead an early-stage discovery project funded by a
patient foundation, towards small molecule therapy for Friedreich’s ataxia
targeting a multi-protein complex. You will work closely with an AI company
in hit finding, and run validation studies to guide compound design through
machine learning (Skills: ITC, SPR, cryo-EM & x-ray, activity assays).

You can find out more about our group here:
https://www.staff.ncl.ac.uk/yuelab/

Any informal enquiries you can contact: wyatt@newcastle.ac.uk





*Wyatt Yue*

Professor of Structural Biology

Biosciences Institute

Faculty of Medical Sciences

Newcastle University NE2 4HH

Group: www.staff.ncl.ac.uk/yuelab/

Profile: wyattyue.github.io



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[ccp4bb] Fwd: [ccpem] registration deadline extended until tomorrow - Cellular Structural Biology & Bioimaging symposium, Oct 26-27, 2021

[Schertler Gebhard (PSI)]

Prof. Gebhard F.X. Schertler
Structural Biology ETH Zürich D-BIOL

Head of Biology and Chemistry
Division
Paul Scherrer Institut
Laboratory of Biomolecular Research,
LBR
OSRA 007
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265

Anfang der weitergeleiteten Nachricht:

Von: Vladimir Korkhov 
Datum: 10. Oktober 2021 um 11:26:23 MESZ
An: cc...@jiscmail.ac.uk
Betreff: [ccpem] registration deadline extended until tomorrow - Cellular 
Structural Biology & Bioimaging symposium, Oct 26-27, 2021
Antwort an: Vladimir Korkhov 

Dear all,

We have extended the deadline to register and submit the abstract for the 
online symposium Cellular Structural Biology & Bioimaging to Monday, 11th of 
October.

The symposium is organised by scientists at PSI, ETH Zurich, University of 
Zurich and University of Bern: 
https://ictac.events.idloom.com/lnb-conference2021

The program of the symposium already includes an outstanding panel of invited 
speakers, as well as the submitted abstracts/poster presentations - many thanks 
to all who have submitted their abstracts! In case you have not yet registered 
or submitted your abstract, we will be happy to receive your registration 
and/or abstract latest by Monday, 11th of October.

Best,
Vladimir Korkhov




Prof. Dr. Volodymyr M. Korkhov

Associate Professor
Institute of Molecular Biology and Biophysics
ETH Zurich

Paul Scherrer Institute
OSRA/001
5232 Villigen PSI, Switzerland
tel: +41 56 310 28 42
e-mail: volodymyr.kork...@psi.ch




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[ccp4bb] Fwd: Building Dna rna duplex

[Shipra Bijpuria]

Hi everyone,

I am working on refinement of a protein-NA complex. It has a dna-rna
duplex. How do we build a dna rna duplex in coot. I was able to optimize
the RNA chain using Rcrane, is there a similar tool to work on DNA chain?

Could anyone please suggest a better way for the refinement of nucleic acid
chains in COOT/CCP4.

Thanks,
Renu



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[ccp4bb] Fwd: asking opinion to all friends here

[Pius Padayatti]

Hi Bulletin members
My question is relatively general regarding some protein engineering

The aim is to design a peptide of approx length 25 nm mostly
helical in nature that can conduct current.
The ends of the peptide have to have some properties that it can
bind to metal electrodes (Ruthenium/palladium).
The current design is a repeat of EAAAR x 33 units flanked on the
N-terminus with a tag (to purify the expressed peptide) and some known gold
binding peptide sequences (QQSWPISGSG). A prediction looks like this will
give what is desired.
Yet, few questions in mind are even the design is to obtain a long helical
structure. A voltage applied is expected to produce a dipole and keep the
peptide to remain mostly as a strand. These are just assumptions.
I want to get this community's valuable suggestions for this design

Questions that would like to get some answers are
1) Does anybody have suggestions for what would be the best design to have
a peptide that can stick to metal surfaces.

2) what can be done to keep a 25 nm long helical peptide not form any
higher-order conformation in solution.

3)Any other ideas people may have here are also welcome

Thank you all in advance and hoping to hear from all of you guys.

Best regards
Padayatti

Note: no crystal structures or any scope to do anything like that is not in
the scope at the moment

-- 
P


-- 
P


-- 
P



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[ccp4bb] Fwd: [ccpem] Glutamate receptor cryo-EM at the MRC LMB

[Krieger, James M]

Hi everyone,

I’m forwarding this position in structural biology and drug development at the 
LMB in Cambridge with my former PhD supervisor, Ingo Greger, in collaboration w 
AstraZeneca in case anyone is interested who is not on CCPEM. It’s a very 
dynamic, interdisciplinary group that I highly recommend.

Believe wishes
James


Begin forwarded message:

From: Ingo Greger 
Date: June 15, 2021 at 07:59:20 GMT+1
To: cc...@jiscmail.ac.uk
Subject: [ccpem] Glutamate receptor cryo-EM at the MRC LMB
Reply-To: i...@mrc-lmb.cam.ac.uk

Hi all

We're looking for a postdoc interested in glutamate receptor structure,
pharmacology and drug development. This is a close collaboration between
the LMB and AstraZeneca, Cambridge:

https://www.nature.com/naturecareers/job/investigator-scientist-medical-research-council-741162

This for 1 year initially with prospect of extension.
Please get in touch for further details: i...@mrc-lmb.cam.ac.uk

References:
Zhang, D., et al. (2021). Gating and modulation of a hetero-octameric AMPA
glutamate receptor
Nature, https://doi.org/10.1038/s41586-021-03613-0

Dohrke, J-N., et al. (2020). Characterizing the binding and function of
TARP8-selective AMPA receptor modulators.
J. Biol. Chem. 295(43):14565-14577

Herguedas, B., et al. (2019). Architecture of the heteromeric GluA1/2 AMPA
receptor in complex with the auxiliary subunit TARP-8.
Science 364(6438): pii: eaav9011.


Best,
Ingo Greger



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[ccp4bb] Fwd: Abstract submission deadline extended to 2 June - PSB Symposium "Frontiers in Bioimaging", 1-2 July 2021

[Daouda Traore]

Dear all,

Please note that the abstract submission deadline for the PSB Symposium 
"Frontiers in Bioimaging" (1-2 July 2021) has been extended to 
*Wednesday 2 June*.


For further information: 
https://www.esrf.fr/home/events/conferences/2021/psb-symposium-frontiers-in-bioimaging/call-for-abstracts-for-poster-and-oral-contributions.html 



Best regards,

Florent

On 2021-04-22 17:28, Florent Bernaudat wrote:

   Dear all,

   The Partnership for Structural Biology (PSB), an alliance of
   research institutes (EMBL, ESRF, IBS and ILL) located in Grenoble,
   France, is pleased to announce that the PSB Symposium "Frontiers in
   Bioimaging" will take place on 1-2 July 2021. The meeting will be
   held remotely on a virtual event platform over two afternoons, and
   will include a series of invited and selected talks, interactive
   virtual posters, and interactive virtual lounges.

   This is to announce that registration is now opened (*It's FREE.*
   *Deadline on 27 June 2021*) and the programme is available.

   All participants are invited to submit an abstract for a poster
   and/or an oral presentation (short talks of 10 minutes). *Submission
   deadline on 2 June 2021*. The number of posters is limited to *50*,
   and best poster prizes (*150 euros each*) will be awarded.

   For further information and to check out the exciting collection of
   invited speakers: https://www.esrf.fr/psbsymposium2021
   

   The aim and scope of this meeting is to highlight progress in 3D
   imaging research that bridges the gap between the atomic and
   cellular scales, with spatial resolutions spanning from subnanometer
   to submicrometer range. Featured topics will include: cryo-electron
   tomography, X-ray tomography, volume electron microscopy, image
   analysis, super-resolution microscopy, and correlative approaches.
   The applications of the above methods to address essential questions
   in life sciences is of particular interest.

   Best regards,

   On behalf of the organising committee

   -- 


   Florent Bernaudat, PhD
   PSB Scientific Coordinator/Animator

   Partnership for Structural Biology
   Carl-Ivar Brändén Building- office 018
   71, Avenue des Martyrs,
   CS 90181
   38042 Grenoble cedex 9
   France

   http://www.psb-grenoble.eu  
   Phone: 33 (0) 476 20 94 08
   Fax: 33 (0) 476 20 94 00




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Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

[rini chaturvedi]

Dear Dr Moriarty,

Thank you so much.

Looking forward for this meeting.

Kind regards,
Rini Chaturvedi



On Thu, Apr 8, 2021 at 12:11 AM Nigel Moriarty  wrote:

> Rini
>
> It appears you are 30 minutes out but it is still early. Phenix Workshops
> will be recorded. As with the last two virtual workshops, they will be
> posted on YouTube. A simple search there will reveal all.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909  Web  : CCI.LBL.gov
> ORCID : orcid.org/-0001-8857-9464
>
>
> On Wed, Apr 7, 2021 at 2:31 AM rini chaturvedi 
> wrote:
>
>> Dear Dr Moriarty,
>>
>> Thank you for sharing the Phenix workshop link.
>>
>> Will it be possible for the recording of the sessions to be shared in the
>> CCP4BB mail?
>>
>> The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45
>> am* in India (*IST*) and it would be difficult for us to be available at
>> that time
>>
>> Kindly let us know if that is a possibility from your end.
>>
>> Kind regards,
>> Rini Chaturvedi
>> Molecular Medicine
>> ICGEB, New Delhi
>>
>>
>> On Mon, Apr 5, 2021 at 10:45 PM Nigel Moriarty 
>> wrote:
>>
>>> Forward in case it was not circulated. Sorry if it's a repeat.
>>>
>>> Cheers
>>>
>>> Nigel
>>>
>>> ---
>>> Nigel W. Moriarty
>>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>>> Lawrence Berkeley National Laboratory
>>> Berkeley, CA 94720-8235
>>> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
>>> Fax   : 510-486-5909  Web  : CCI.LBL.gov
>>> ORCID : orcid.org/-0001-8857-9464
>>>
>>>
>>> -- Forwarded message -
>>> From: Paul Adams 
>>> Date: Wed, Mar 31, 2021 at 2:08 PM
>>> Subject: Please register - Phenix Workshops - April 7 & 14
>>> To: PHENIX user mailing list 
>>> Cc: Nigel Moriarty , Ashley Dawn ,
>>> CCP4BB@JISCMAIL.AC.UK 
>>>
>>>
>>> Dear Colleagues,
>>>
>>> The Phenix developers will be holding an online *Phenix User Workshop on
>>> the 7th and 14th of April at 4-9pm PDT.* These times will work best for
>>> researchers in Asia and Australasia.
>>>
>>> The format of the workshop will be demos of the use of Phenix programs
>>> combined with slides to explain the theory. We expect an interactive
>>> meeting where attendees can ask questions for the Phenix team to answer.
>>>
>>> The workshop will cover aspects of macromolecular crystallography
>>> in Phenix, with the final emphasis based on the applicants’ research
>>> interests. To apply please fill out this form
>>> . We will make every effort to
>>> accommodate all applicants, but may need to defer some requests to a
>>> future workshop if demand is high. We are hoping this workshop will be a
>>> success, in which case we plan to host more in the future.
>>>
>>> *AGENDA:*
>>> *7 APR *
>>>
>>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>>- 4.00pm - Paul Adams - Phenix Overview
>>>- 4.30pm - Tom Terwilliger - Map Improvement
>>>- 5.45pm - Tom Terwilliger - Model Building
>>>- 7.00pm - Question/Answer session
>>>
>>> *14 APR *
>>>
>>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>>- 4.00pm - Pavel Afonine - Real Space Refine
>>>- 5.15pm - Nigel Moriarty - Ligands and Restraints
>>>- 6.00pm - Jane Richardson - Validation
>>>- 7.00pm - Question/Answer session
>>>
>>>
>>> Cheers,
>>> The Phenix Developer Team
>>>
>>> --
>>> Paul Adams
>>> Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
>>> http://biosciences.lbl.gov/divisions/mbib)
>>> Principal Investigator, Computational Crystallography Initiative, LBL (
>>> http://cci.lbl.gov)
>>> Vice President for Technology, the Joint BioEnergy Institute (
>>> http://www.jbei.org)
>>> Principal Investigator, ALS-ENABLE, Advanced Light Source (
>>> http://als-enable.lbl.gov)
>>> Division Deputy for Biosciences, Advanced Light Source (
>>> https://als.lbl.gov)
>>> Laboratory Research Manager, ENIGMA Science Focus Area (
>>> http://enigma.lbl.gov)
>>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
>>> http://bioeng.berkeley.edu)
>>> Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
>>> http://compbiochem.berkeley.edu)
>>>
>>> Building 33, Room 347
>>> Building 978, Room 4126
>>> Building 977, Room 180C
>>> Tel: 1-510-486-4225
>>> http://cci.lbl.gov/paul
>>>
>>> Lawrence Berkeley Laboratory
>>> 1 Cyclotron Road
>>> BLDG 33R0345
>>> Berkeley, CA 94720, USA.
>>>
>>> Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov
>>>  ] [ 1-510-486-5455 ]
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>

Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

[Nigel Moriarty]

Rini

It appears you are 30 minutes out but it is still early. Phenix Workshops
will be recorded. As with the last two virtual workshops, they will be
posted on YouTube. A simple search there will reveal all.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Wed, Apr 7, 2021 at 2:31 AM rini chaturvedi 
wrote:

> Dear Dr Moriarty,
>
> Thank you for sharing the Phenix workshop link.
>
> Will it be possible for the recording of the sessions to be shared in the
> CCP4BB mail?
>
> The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45
> am* in India (*IST*) and it would be difficult for us to be available at
> that time
>
> Kindly let us know if that is a possibility from your end.
>
> Kind regards,
> Rini Chaturvedi
> Molecular Medicine
> ICGEB, New Delhi
>
>
> On Mon, Apr 5, 2021 at 10:45 PM Nigel Moriarty  wrote:
>
>> Forward in case it was not circulated. Sorry if it's a repeat.
>>
>> Cheers
>>
>> Nigel
>>
>> ---
>> Nigel W. Moriarty
>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
>> Fax   : 510-486-5909  Web  : CCI.LBL.gov
>> ORCID : orcid.org/-0001-8857-9464
>>
>>
>> -- Forwarded message -
>> From: Paul Adams 
>> Date: Wed, Mar 31, 2021 at 2:08 PM
>> Subject: Please register - Phenix Workshops - April 7 & 14
>> To: PHENIX user mailing list 
>> Cc: Nigel Moriarty , Ashley Dawn ,
>> CCP4BB@JISCMAIL.AC.UK 
>>
>>
>> Dear Colleagues,
>>
>> The Phenix developers will be holding an online *Phenix User Workshop on
>> the 7th and 14th of April at 4-9pm PDT.* These times will work best for
>> researchers in Asia and Australasia.
>>
>> The format of the workshop will be demos of the use of Phenix programs
>> combined with slides to explain the theory. We expect an interactive
>> meeting where attendees can ask questions for the Phenix team to answer.
>>
>> The workshop will cover aspects of macromolecular crystallography
>> in Phenix, with the final emphasis based on the applicants’ research
>> interests. To apply please fill out this form
>> . We will make every effort to
>> accommodate all applicants, but may need to defer some requests to a
>> future workshop if demand is high. We are hoping this workshop will be a
>> success, in which case we plan to host more in the future.
>>
>> *AGENDA:*
>> *7 APR *
>>
>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>- 4.00pm - Paul Adams - Phenix Overview
>>- 4.30pm - Tom Terwilliger - Map Improvement
>>- 5.45pm - Tom Terwilliger - Model Building
>>- 7.00pm - Question/Answer session
>>
>> *14 APR *
>>
>>- 3.45pm - Start of Zoom session (for people to debug any issues)
>>- 4.00pm - Pavel Afonine - Real Space Refine
>>- 5.15pm - Nigel Moriarty - Ligands and Restraints
>>- 6.00pm - Jane Richardson - Validation
>>- 7.00pm - Question/Answer session
>>
>>
>> Cheers,
>> The Phenix Developer Team
>>
>> --
>> Paul Adams
>> Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
>> http://biosciences.lbl.gov/divisions/mbib)
>> Principal Investigator, Computational Crystallography Initiative, LBL (
>> http://cci.lbl.gov)
>> Vice President for Technology, the Joint BioEnergy Institute (
>> http://www.jbei.org)
>> Principal Investigator, ALS-ENABLE, Advanced Light Source (
>> http://als-enable.lbl.gov)
>> Division Deputy for Biosciences, Advanced Light Source (
>> https://als.lbl.gov)
>> Laboratory Research Manager, ENIGMA Science Focus Area (
>> http://enigma.lbl.gov)
>> Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
>> http://bioeng.berkeley.edu)
>> Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
>> http://compbiochem.berkeley.edu)
>>
>> Building 33, Room 347
>> Building 978, Room 4126
>> Building 977, Room 180C
>> Tel: 1-510-486-4225
>> http://cci.lbl.gov/paul
>>
>> Lawrence Berkeley Laboratory
>> 1 Cyclotron Road
>> BLDG 33R0345
>> Berkeley, CA 94720, USA.
>>
>> Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov  ]
>> [ 1-510-486-5455 ]
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>



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Re: [ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

[rini chaturvedi]

Dear Dr Moriarty,

Thank you for sharing the Phenix workshop link.

Will it be possible for the recording of the sessions to be shared in the
CCP4BB mail?

The given time for the workshop i.e *3.45 pm PDT* which will be around *3.45
am* in India (*IST*) and it would be difficult for us to be available at
that time

Kindly let us know if that is a possibility from your end.

Kind regards,
Rini Chaturvedi
Molecular Medicine
ICGEB, New Delhi


On Mon, Apr 5, 2021 at 10:45 PM Nigel Moriarty  wrote:

> Forward in case it was not circulated. Sorry if it's a repeat.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909  Web  : CCI.LBL.gov
> ORCID : orcid.org/-0001-8857-9464
>
>
> -- Forwarded message -
> From: Paul Adams 
> Date: Wed, Mar 31, 2021 at 2:08 PM
> Subject: Please register - Phenix Workshops - April 7 & 14
> To: PHENIX user mailing list 
> Cc: Nigel Moriarty , Ashley Dawn ,
> CCP4BB@JISCMAIL.AC.UK 
>
>
> Dear Colleagues,
>
> The Phenix developers will be holding an online *Phenix User Workshop on
> the 7th and 14th of April at 4-9pm PDT.* These times will work best for
> researchers in Asia and Australasia.
>
> The format of the workshop will be demos of the use of Phenix programs
> combined with slides to explain the theory. We expect an interactive
> meeting where attendees can ask questions for the Phenix team to answer.
>
> The workshop will cover aspects of macromolecular crystallography
> in Phenix, with the final emphasis based on the applicants’ research
> interests. To apply please fill out this form
> . We will make every effort to
> accommodate all applicants, but may need to defer some requests to a
> future workshop if demand is high. We are hoping this workshop will be a
> success, in which case we plan to host more in the future.
>
> *AGENDA:*
> *7 APR *
>
>- 3.45pm - Start of Zoom session (for people to debug any issues)
>- 4.00pm - Paul Adams - Phenix Overview
>- 4.30pm - Tom Terwilliger - Map Improvement
>- 5.45pm - Tom Terwilliger - Model Building
>- 7.00pm - Question/Answer session
>
> *14 APR *
>
>- 3.45pm - Start of Zoom session (for people to debug any issues)
>- 4.00pm - Pavel Afonine - Real Space Refine
>- 5.15pm - Nigel Moriarty - Ligands and Restraints
>- 6.00pm - Jane Richardson - Validation
>- 7.00pm - Question/Answer session
>
>
> Cheers,
> The Phenix Developer Team
>
> --
> Paul Adams
> Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
> http://biosciences.lbl.gov/divisions/mbib)
> Principal Investigator, Computational Crystallography Initiative, LBL (
> http://cci.lbl.gov)
> Vice President for Technology, the Joint BioEnergy Institute (
> http://www.jbei.org)
> Principal Investigator, ALS-ENABLE, Advanced Light Source (
> http://als-enable.lbl.gov)
> Division Deputy for Biosciences, Advanced Light Source (
> https://als.lbl.gov)
> Laboratory Research Manager, ENIGMA Science Focus Area (
> http://enigma.lbl.gov)
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
> http://bioeng.berkeley.edu)
> Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
> http://compbiochem.berkeley.edu)
>
> Building 33, Room 347
> Building 978, Room 4126
> Building 977, Room 180C
> Tel: 1-510-486-4225
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 33R0345
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov  ]
> [ 1-510-486-5455 ]
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Fwd: Thank you for registering - Phenix Workshops - April 7 & 14

[Nigel Moriarty]

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


-- Forwarded message -
From: Ashley Dawn 
Date: Mon, Apr 5, 2021 at 9:56 AM
Subject: Thank you for registering - Phenix Workshops - April 7 & 14
To: Ashley Dawn 
Cc: Nigel Moriarty , Christopher Schlicksup <
cjschlick...@lbl.gov>, phenixdev 


Good morning,

Thank you for registering for the Phenix Workshops that begin this
Wednesday.

*AGENDA: *
*7 APR  *(click to add to google calendar)


   - 3.45pm - Start of Zoom session (for people to debug any issues)
   - 4.00pm - Paul Adams - Phenix Overview
   - 4.30pm - Tom Terwilliger - Map Improvement
   - 5.45pm - Tom Terwilliger - Model Building
   - 7.00pm - Question/Answer session

*14 APR * (click to add to google calendar)


   - 3.45pm - Start of Zoom session (for people to debug any issues)
   - 4.00pm - Pavel Afonine - Real Space Refine
   - 5.15pm - Nigel Moriarty - Ligands and Restraints
   - 6.00pm - Jane Richardson - Validation
   - 7.00pm - Question/Answer session


Cheers,
The Phenix Developer Team
Ashley Dawn (she/her/hers) [image: A button for name playback in email
signature] 
Senior Administrator
Molecular Biophysics & Integrated Bioimaging
Lawrence Berkeley Laboratory
1-510-486-5455



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[ccp4bb] Fwd: Please register - Phenix Workshops - April 7 & 14

[Nigel Moriarty]

Forward in case it was not circulated. Sorry if it's a repeat.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


-- Forwarded message -
From: Paul Adams 
Date: Wed, Mar 31, 2021 at 2:08 PM
Subject: Please register - Phenix Workshops - April 7 & 14
To: PHENIX user mailing list 
Cc: Nigel Moriarty , Ashley Dawn ,
CCP4BB@JISCMAIL.AC.UK 


Dear Colleagues,

The Phenix developers will be holding an online *Phenix User Workshop on
the 7th and 14th of April at 4-9pm PDT.* These times will work best for
researchers in Asia and Australasia.

The format of the workshop will be demos of the use of Phenix programs
combined with slides to explain the theory. We expect an interactive
meeting where attendees can ask questions for the Phenix team to answer.

The workshop will cover aspects of macromolecular crystallography
in Phenix, with the final emphasis based on the applicants’ research
interests. To apply please fill out this form
. We will make every effort to
accommodate all applicants, but may need to defer some requests to a
future workshop if demand is high. We are hoping this workshop will be a
success, in which case we plan to host more in the future.

*AGENDA:*
*7 APR *

   - 3.45pm - Start of Zoom session (for people to debug any issues)
   - 4.00pm - Paul Adams - Phenix Overview
   - 4.30pm - Tom Terwilliger - Map Improvement
   - 5.45pm - Tom Terwilliger - Model Building
   - 7.00pm - Question/Answer session

*14 APR *

   - 3.45pm - Start of Zoom session (for people to debug any issues)
   - 4.00pm - Pavel Afonine - Real Space Refine
   - 5.15pm - Nigel Moriarty - Ligands and Restraints
   - 6.00pm - Jane Richardson - Validation
   - 7.00pm - Question/Answer session


Cheers,
The Phenix Developer Team

-- 
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
http://biosciences.lbl.gov/divisions/mbib)
Principal Investigator, Computational Crystallography Initiative, LBL (
http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute (
http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source (
http://als-enable.lbl.gov)
Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (
http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
http://bioeng.berkeley.edu)
Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
http://compbiochem.berkeley.edu)

Building 33, Room 347
Building 978, Room 4126
Building 977, Room 180C
Tel: 1-510-486-4225
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov  ]
[ 1-510-486-5455 ]



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[ccp4bb] Fwd: [ccp4bb] Co-crystallization and thermal shift assay

[mesters]

Hello,

we had an interesting case in the lab many years ago... Using the 
shift-assay, a student managed to identify conditions that markedly 
stabilized the protein of interest. To cut a long story short, in the 
end it turned out conditions were identified that gave monomers while 
the biological active unit is clearly multimeric! Actually, the monomer 
never crystallized while the multimer did...


Keep in mind that a compound may induce a structural change and that the 
resulting structure may indeed be less stable. An increase in ΔTm would 
certainly "desirable" but this alone is not to be used as a measure. If 
you are interested in the complex, a more important parameter will be 
the affinity of the compound for the protein. Example, let's assume the 
affinity is about 50 µM, then you will need at least 10 times that value 
in the crystallization droplet to achieve about 90% occupation. Problem 
may be with concentrations > 1 mM, you can not achieve that high 
concentration in the solute and will have to add for example DMSO which 
may in turn have negative efefcts on your protein of interest. 
Furthermore, strange scenarios could be, the compound itself interferes 
in protein-protein contact formation at higher concentrations or, could 
promote protein-protein contact formation (work as a glue) and not show 
up in the active site at all...


Question in the end will be not about ΔTm (which is one useful tool for 
identifying buffers or compounds worth using/testing), but whether the 
complex can in fact be co-crystallized (the ultimate "test"!).  So yes, 
go ahead and test it.


Best,

Jeroen

--
*Dr.math. et dis. nat.Jeroen R. Mesters*
Deputy, Lecturer, Program Coordinator /Infection Biology
/ 
Visiting 
Professorship (South Bohemian University) in Biophysics

*University of Lübeck*
Center for Structural and Cell Biology in Medicine
*Institute of Biochemistry*

Tel +49 451 3101 3105 (secretariate 3101)
Fax +49 451 3101 3104
jeroen.mest...@uni-luebeck.de 
www.biochem.uni-luebeck.de 

*Ratzeburger Allee 160
23538 Lübeck, Schleswig-Holstein
Germany*

Am 25.02.21 um 15:55 schrieb Saif Mohd:

Hello everyone,

1) How much change in Tm (ΔTm) in a thermal shift assay is considered 
to be significant ?


2) A negative  ΔTm infers that the compound is making the protein 
unstable. In such a case, will the co-crystallization be difficult or 
just impossible or on the contrary it shouldn't matter much?



Thanks and best regards,
Saif




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[ccp4bb] Fwd: Fw: Human Resources Advertisement: Lecturer/Lecturer below the bar in Protein Biochemistry

[Tewfik Soulimane]

 Dear all



I'd like to draw attention of interested candidates to the opportunity as
listed below.



We are targeting excellent candidates in protein biochemistry,
bioinformatics or bioprocessing.


Yours sincerely


*Professor Tewfik Soulimane*

Head of School, Natural Sciences

Head of Department, Chemical Sciences

*T*  +353 (0) 61 234133

*M*  +353 (0) 86 1238746*ul.ie/~ces  *





University of Limerick, Limerick, V94 T9PX

Ollscoil Luimnigh, V94 T9PX, Éire



[image: Chemical-Sciences-sigLogo (2)]

[image: Chemical-Sciences-athena (4)]




[image: cid:image019.png@01D588CF.58D37AC0]   [image:
cid:image020.png@01D588CF.58D37AC0]   [image:
cid:image021.png@01D588CF.58D37AC0]   [image:
cid:image022.png@01D588CF.58D37AC0]   [image:
cid:image023.png@01D588CF.58D37AC0]   [image:
cid:image024.png@01D588CF.58D37AC0]



--
*From:* eRecruitment 
*Sent:* Monday 8 February 2021 14:39
*To:* HRNotices 
*Subject:* Human Resources Advertisement: Lecturer/Lecturer below the bar
in Protein Biochemistry




The University of Limerick (UL) with over 16,300 students and 1,700 staff
is an energetic and enterprising institution with a proud record of
innovation and excellence in education, research and scholarship. The
dynamic, entrepreneurial and pioneering values which drive UL’s mission and
strategy ensure that we capitalise on local, national and international
engagement and connectivity. We are renowned for providing an outstanding
student experience and employability and conducting leading edge research.
Our commitment is to make a difference by shaping the future through
educating and empowering our undergraduate and postgraduate students. UL is
situated on a superb riverside campus of over 130 hectares with the River
Shannon as a unifying focal point. Outstanding recreational, cultural and
sporting facilities further enhance this exceptional learning and research
environment.



Applications are invited for the following position:



*Faculty of Science & Engineering*



*School of Natural Sciences*



*Department of Chemical Sciences*



Lecturer/Lecturer below the bar in Protein Biochemistry



Contract Type: Tenure Track (five year fixed term). During the term of the
contract the successful applicant will have the opportunity to apply for
tenure in accordance with the University's Policy and Procedures for
Granting Multi-annual Status to Tenure Track Academic Staff




Salary Scale:   Lecturer: €54,162 - €86,181 p.a. pro rata

Lecturer below the bar: €40,599 - €55,818 p.a. pro
rata



Further information for applicants and application material is available
online from:

http://www.ul.ie/hrvacancies/



The closing date for receipt of applications is *Monday, 8th March 2021.*

Applications must be completed online before *12 noon, Irish Standard Time*
on the closing date.



*Please email **erecruitm...@ul.ie* * if you experience
any difficulties*



*Applications are welcome from suitably qualified candidates.*

*The University of Limerick holds a Bronze Athena SWAN award in recognition
of our commitment to advancing equality in higher education. The University
is an equal opportunities employer and is committed to selection on merit
welcoming applicants from all sections of the community. The University has
a range of initiatives to support a family friendly working environment,
including flexible working.*



“The University of Limerick has implemented a “Smoke and Vape Free Campus
Policy”.  Smoking and vaping in all forms is prohibited.”



*[image: HR excellence in research]*   
  [image: Image result for ECU Gender Charter Logo]



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[ccp4bb] Fwd: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)

[Mark J van Raaij]

in case it might be of interest for someone @CNB:


> Begin forwarded message:
> 
> From: Bjørn Panyella Pedersen 
> Subject: [ccp4bb] Postdoc position, Plant Hormone Transporting Membrane 
> Proteins (Denmark)
> Date: 5 February 2021 at 17:20:38 GMT+1
> To: CCP4BB@JISCMAIL.AC.UK
> Reply-To: Bjørn Panyella Pedersen 
> 
> Dear colleagues,
> I have an open postdoc position funded by the ERC (details below).
> Please pass this along to anyone who might be interested. Thanks!
> /Bjørn
> 
> Postdoctoral position in Structure of Plant Hormone Transporting Membrane 
> Proteins at Aarhus University, Denmark.
> 
> online posting:
> https://tinyurl.com/MBGpostdoc 
> 
> We are looking for a highly skilled and motivated postdoc with an interest in 
> working on plant hormone transporting membrane transporters and preferably 
> with a proven track record in the area of structural and/or functional 
> analysis of membrane proteins and an interest for plant biology.
> 
> Starting date is negotiable. Funding is available through an ERC grant for at 
> least 2 years of employment. An extension is possible for up to a total 
> maximum of 4 years of employment as a postdoc.
> 
> The position:
> The position seeks to strengthen ongoing activities in the laboratory of 
> Bjørn P. Pedersen on structure, related to the function and mechanism of 
> plant hormone-transporting membrane proteins as defined by the ERC project 
> MUM-GROW (pedersenlab.dk ). Exact project will be 
> shaped out in dialogue with top runners. The laboratory's interest is the 
> interplay between structure and function of transmembrane transport processes 
> with a focus on metabolite uptake systems, and the methods uses are primarily 
> crystallography and cryo-EM. The group is part of the Section of Structural 
> Biology at Aarhus University.
> 
> The candidate:
> A successful candidate has a relevant Ph.D. degree and a solid and documented 
> background in structural biology, biochemistry and/or biophysics. Experience 
> with membrane protein expression and purification is favored, and the 
> candidate must demonstrate an ability and interest to work with membrane 
> proteins with a structural aim. Applicants should be ambitious, show strong 
> collaborative skills, and be able to take initiatives and responsibility 
> within the work environment.
> 
> The successful candidate is offered:
> - access to a well-developed research infrastructure.
> - a research climate inviting lively, open and critical discussion within and 
> across different fields of research.
> - a working environment with teamwork, close working relations, network 
> activities among young scientists and social activities.
> - a workplace characterized by professionalism, equality and a healthy 
> work-life balance.
> 
> The city:
> In Aarhus you have easy access to beautiful nature, an exciting culture and 
> city life as well as a safe environment for children - a great place for the 
> whole family. The city of Aarhus has everything you need: exciting national 
> and international jobs, delightful residential areas, a rich cultural life, 
> and beautiful surrounding landscape of woods and coastline that make Aarhus a 
> wonderful place to live and work. See https://international.au.dk/life/ 
>  for details. Aarhus University offers 
> relocation service to international researchers. You can read more about it 
> at https://international.au.dk/life/researcherscomingtoau/ 
> .
> 
> Deadline:
> All applications must be made online (https://tinyurl.com/MBGpostdoc 
> ) and received by March 1st 2021.
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Fwd: CCP4i2 Export and Deposition task

[Jon Cooper]

Hello, if you are depositing the structure, a workaround might just be to use:

https://pdb-extract.wwpdb.org/

I suspect that was obvious, sorry!

Cheers, Jon. Cooper

 Original Message 
On 26 Nov 2020, 17:56, Nikolas wrote:

> Hi all,
>
> I am trying to prepare and export the files for a structure solved in CCP4i2 
> but so far the only tasks available are the "Prepare and validate" and "Merge 
> experimental data .." tasks. I have tried to look for the tutorial but both 
> the icon and the input page illustrated are different from the ones I can see 
> in the software.
>
> I guess I might be missing the whole part of it since the PDB icon shown in 
> the task documentation is missing.
>
> Any suggestions/ideas?
>
> Many thanks,
> Nikolas
>
> ---
>
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Re: [ccp4bb] Fwd: CCP4i2 Export and Deposition task

[Joel Sussman]

Dear Nikolas
I have the exact same problem
Joel


On Nov 26, 2020, at 20:00, Nikolas  wrote:


Hi all,

I am trying to prepare and export the files for a structure solved in CCP4i2 
but so far the only tasks available are the "Prepare and validate" and "Merge 
experimental data .." tasks. I have tried to look for the tutorial but both the 
icon and the input page illustrated are different from the ones I can see in 
the software.

I guess I might be missing the whole part of it since the PDB icon shown in the 
task documentation is missing.

Any suggestions/ideas?

Many thanks,
Nikolas




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[ccp4bb] Fwd: CCP4i2 Export and Deposition task

[Nikolas]

Hi all,

I am trying to prepare and export the files for a structure solved in
CCP4i2 but so far the only tasks available are the "Prepare and validate"
and "Merge experimental data .." tasks. I have tried to look for the
tutorial but both the icon and the input page illustrated are different
from the ones I can see in the software.

I guess I might be missing the whole part of it since the PDB icon shown in
the task documentation is missing.

Any suggestions/ideas?

Many thanks,
Nikolas



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[ccp4bb] Fwd: CCP4i2 Export and Deposition task

[Nikolas]

Hi all,

I am trying to prepare and export the files for a structure solved in
CCP4i2 but so far the only tasks available are the "Prepare and validate"
and "Merge experimental data .." tasks. I have tried to look for the
tutorial but both the icon and the input page illustrated are different
from the ones I can see in the software.

I guess I might be missing the whole part of it since the PDB icon shown in
the task documentation is missing.

Any suggestions/ideas?

Many thanks,
Nikolas



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[ccp4bb] Fwd: [ccp4bb] AW: Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

[Patrick Loll]

Agreed. In fact, as a matter of course, when die Rechnung arrives I endeavor to 
head for die Tur…

> 
> 
> 
>> On 20 Oct 2020, at 10:23 AM, Schreuder, Herman /DE 
>>  wrote:
>> 
>> Looks more like crowd-phishing to me! 
>> The original message did not make it through my spam filter and it may not 
>> be a good idea to open the shared file.
>> Herman
>> 
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board  Im Auftrag von Robbie 
>> Joosten
>> Gesendet: Dienstag, 20. Oktober 2020 16:16
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 
>> 'Rechnungen' ein.
>> 
>> Working on your bills with the entire bulletin board. Is that crowdsourcing 
>> or what? 
>> 
>>> -Original Message-
>>> From: CCP4 bulletin board  On Behalf Of Kevin 
>>> Denkmann
>>> Sent: Tuesday, October 20, 2020 15:27
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 
>>> 'Rechnungen' ein.
>>> 
>>> 
>>> Kevin Denkmann shared a file with you
>>> 
>>> Here's the document that Kevin Denkmann shared with you.
>>> 
>>> >> my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
>>> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
>>> Rechnungen
>>> This link will work for anyone.
>>> Open >> my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
>>> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
>>> 
>>> Privacy Statement >> notifyp.svc.ms:443/api/v2/tracking/method/Click?mi=HgrSi7OfwUKiTn-
>>> 401hPpQ=PrivacyStatement=f97d4ae4336b3342c9a937ee3f36e84e
>>> u=https%3a%2f%2fprivacy.microsoft.com%2fprivacystatement%5c>
>>> >> notifyp.svc.ms:443/api/v2/tracking/method/View?mi=HgrSi7OfwUKiTn-
>>> 401hPpQ>
>>> 
>>> 
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
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>>> jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1d
>>> ata=02%7C01%7CHerman.Schreuder%40SANOFI.COM%7Cf86f5afb3c3d4664586e08d8
>>> 7502dc60%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C6373880027010674
>>> 74sdata=fR1KagWSgefPDCTSYiUFKOQKdWgRFUB7ysSaCe8JrTI%3Dreserv
>>> ed=0
>> 
>> 
>> 
>> 
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> 
> Patrick Loll
> pjl...@gmail.com
> 
> 
> 

Patrick Loll
pjl...@gmail.com



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[ccp4bb] Fwd: Call for MX beamtime proposals at HZB, BESSY II, deadline extended to September 06, 2020

[Manfred S. Weiss]

Dear all,


the next MX-proposal application deadline has been extenden to September 06, 
2020

As usual, all proposals will be handled by our electronic user portal GATE,
https://www.helmholtz-berlin.de/pubbin/hzbgate

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(03/2021-08/2021).

In order to apply for beamtime, please register in GATE and submit
a new beam time application proposal.

Please note that we now expect from each research group only ONE proposal,
which can contain up to 20 individual projects.


IMPORTANT: If you have a running 2019-1 or a running 2020-1 proposal, you
may ask for extension. For a 2020-1 proposal, an interim report is necessary,
and for a 2019-1 proposal a full report including highlights. You will also
be able to edit and modify your proposals by adding and deleting projects.


HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations in
Germany with more than 3300 PDB depositions in total. Beamtime is granted
based on the reviewed proposals and on reports from previous research
activities. Please make sure to include them if available.

Experimental setup:

BL14.1:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.8x10¹¹ Phot/sec x 100 mA at sample position
 (0.04-1 sec exposure time per frame)
- PILATUS3 S 6M detector with 1000 µm Si sensor thickness, 141 mm-680 mm max. 
distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
IMPORTANT: this will be upgraded to UNIPUCKS only in September 2020
- User defined beam shaping from 50 µm-100 µm diameter possible
- In situ crystal-screening using 96-well plates
- 32-core XEON-CPU server, with 10GB uplink to Pilatus 6M
- Data collection control via MXCuBE2
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out UV-RIP experiments at BL14.1. For further information,
please visit:
https://www.helmholtz-berlin.de/forschung/oe/np/gmx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon energy range: 5.5-16 keV (wavelength: 0.775-2.25 A)
- Photon flux: 1.6x10¹¹ Phot/sec x 100 mA at sample position
 (0.05-1 sec exposure time per frame)
- PILATUS3 S 2M detector with 1000 µm Si sensor thickness,
 85 mm - 800 mm distance from the sample (a special mode with
 56 mm distance is also available upon request)
- Nanodiffractometer with fast air-bearing axis and on-axis sample
 microscope
- User defined beam shaping from 30 µm-150 µm diameter possible
- Data collection control via MXCuBE2
- G-ROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- AMPTEK-XRF detector and XFEPLOT software available
- UV-Microsprectrophotometer offline setup available

If you need atomic resolution or better, BL14.2 is the beamline
of choice for you!!

BL14.3:
- Fixed photon energy: 13.8 keV (wavelength: 0.89 A)
- Photon flux: 1.6x10exp10 Phot/sec x 100mA at sample position
 (3-20 sec exposure time per frame)
- PILATUS 6M detector, 54 mm-450 mm distance from the sample
- MD2S microdiffractometer with mini-kappa goniometer
- In situ crystal-screening using 96-well plates
- RT data collection
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Data collection control via MXCuBE2
- Common MX software installed including EDNA, XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- REX rapid nozzle exchanger
- HC-Lab dehydration device installed (please specify HC-Lab-beamtime
 in your proposal if needed)
- AMPTEK-XRF detector and XFEPLOT software available

Other facilities:
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpix CCD-camera
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)

S1-biolab facilities (separate registration required):
- Protein production and purification (AEKTA)
- nL 96-well crystallization plate formulation and storage at
 5°C and 20°C
- Biophysical characterization with real time PCR (thermofluor assay)
- Contactless compound pipetting using ATS

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening 

Re: [ccp4bb] Fwd: Refmac error

[Robbie Joosten]

Hi Eugene,

We recently had this with a student as well and at least in PDB format the 
files are salvageable by doing a simple search and replace from , to .

Rather than going completely American, you can also just change the number 
format. In Windows 10 this is 
Settings > Time & Language > Data, time, & regional formatting (hidden on the 
right) > Additional data, time, & regional settings > Change data, time, or 
number formats > Additional settings

Only "decimal symbol" and "Digit grouping symbol" need to be set to . and , 
respectively. 

Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eugene
> Krissinel
> Sent: Friday, May 29, 2020 12:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Fwd: Refmac error
> 
> Dear Nadine,
> 
> Many thanks for sharing your project with me on CCP4 Cloud. The reason for
> Refmac failure is absolutely clear: the previous Coot job exported PDB file,
> using commas (wie im besten Deutsch) instead of periods (as we would
> expect in best English) for all float-point numbers. You can see it if you go 
> to
> the previous Coot job report, scroll down to "Output Structure", press
> "Display" and scroll down a bit.
> 
> This effect is known to be peculiar to WinCoot -- have you used Windows
> machine to run Coot in job 179? And had you used a different machine to
> run Coot in job 169, which produced output file in correct format?
> 
> The only way to cope with the situation, known to me, is to ensure that your
> Windows machine uses US/English locale settings. This takes tweaking
> Language settings in Windows Control Panel and rebooting the machine.
> Regrettably, you will have to repeat job 179 in new locale. If it contains
> particularly valuable results that are difficult to reproduce, let me know 
> and I
> will advise you of the rescue procedure.
> 
> Admittedly, you are by far not the only one who encounters this problem,
> which appears in all locales with float point formats different from
> US/English. Therefore, I cc WinCoot developer on this email (they are aware
> anyway, and are working on the issue), as well as CCP4 BB list, where you
> placed your request initially, for other CCP4 users to be aware of this
> feature. And there is an obvious homework for us here at CCP4.
> 
> Once again, many thanks for your report. Please unshare this project now
> (simply remove my login name where you have put it for sharing before).
> 
> Kind regards,
> 
> Eugene
> 
> 
> On Fri, May 29, 2020 at 9:52 AM Nadine Gerlach  <mailto:ngerl...@marum.de> > wrote:
> 
> 
>   Hey Eugene,
> 
>   actually this happend not just for one project of mine, but I shared
> one project with you now. Scroll down to the last refmac run after model
> building with coot. I just tried it again but it is still the same result.
> 
>   Thanks for the help!!
> 
>   Nadine
> 
> 
> 
> 
> 
>   Am 28.05.2020 um 19:28 schrieb Eugene Krissinel:
> 
> 
>   Dear Nadine,
> 
>   We would need more information on what happens. You can
> share your project with me and I can have a look at it. To share the project,
> open it, then push Main Manu button in top-left corner, choose "Share" and
> set my login name (eugene), then confirm to me by e-mail. Your data and
> project will be treated as confidential.
> 
>   Many thanks for writing to us (use c...@ccp4.ac.uk
> <mailto:c...@ccp4.ac.uk>  rather than BB list for this type of queries please)
> 
>   Eugene
> 
> 
>   -- Forwarded message -
>   From: Nadine Gerlach  <mailto:ngerl...@marum.de> >
>   Date: Thu, 28 May 2020 at 14:21
>   Subject: Refmac error
>   To: mailto:CCP4BB-
> requ...@jiscmail.ac.uk> >
> 
> 
> 
> 
>   Hey everybody,
> 
>   I am running refmac in CCP4 ccloud after Coot and I get this
> error message:
> 
>*** error running refmac5: Error in command.call
>   Return code: 512
> 
>   Any held is really appreaciated!
> 
>   Best wishes,
>   Nadine
>   --
>   Nadine Gerlach
>   PhD candidate
>   MPG MARUM Bridge Group Marine Glycobiology
>   MARUM, University Bremen & Max Planck Institute for
> Marine Microbiology
>   Tel: +49 421 218-65758
>   Email: nger­lach@mpi-bre­men.de <http://men.de> ,
> ngerl...@marum.de <mailto:ngerl...@marum.de>
>   MAR

Re: [ccp4bb] Fwd: Refmac error

[Eugene Krissinel]

Dear Nadine,

Many thanks for sharing your project with me on CCP4 Cloud. The reason for
Refmac failure is absolutely clear: the previous Coot job exported PDB
file, using commas (wie im besten Deutsch) instead of periods (as we would
expect in best English) for all float-point numbers. You can see it if you
go to the previous Coot job report, scroll down to "Output Structure",
press "Display" and scroll down a bit.

This effect is known to be peculiar to WinCoot -- have you used Windows
machine to run Coot in job 179? And had you used a different machine to run
Coot in job 169, which produced output file in correct format?

The only way to cope with the situation, known to me, is to ensure that
your Windows machine uses US/English locale settings. This takes tweaking
Language settings in Windows Control Panel and rebooting the machine.
Regrettably, you will have to repeat job 179 in new locale. If it contains
particularly valuable results that are difficult to reproduce, let me know
and I will advise you of the rescue procedure.

Admittedly, you are by far not the only one who encounters this problem,
which appears in all locales with float point formats different from
US/English. Therefore, I cc WinCoot developer on this email (they are aware
anyway, and are working on the issue), as well as CCP4 BB list, where you
placed your request initially, for other CCP4 users to be aware of this
feature. And there is an obvious homework for us here at CCP4.

Once again, many thanks for your report. Please unshare this project now
(simply remove my login name where you have put it for sharing before).

Kind regards,

Eugene


On Fri, May 29, 2020 at 9:52 AM Nadine Gerlach  wrote:

> Hey Eugene,
>
> actually this happend not just for one project of mine, but I shared one
> project with you now. Scroll down to the last refmac run after model
> building with coot. I just tried it again but it is still the same result.
>
> Thanks for the help!!
>
> Nadine
>
>
> Am 28.05.2020 um 19:28 schrieb Eugene Krissinel:
>
> Dear Nadine,
>
> We would need more information on what happens. You can share your project
> with me and I can have a look at it. To share the project, open it, then
> push Main Manu button in top-left corner, choose "Share" and set my login
> name (eugene), then confirm to me by e-mail. Your data and project will be
> treated as confidential.
>
> Many thanks for writing to us (use c...@ccp4.ac.uk rather than BB list
> for this type of queries please)
>
> Eugene
>
>
> -- Forwarded message -
> From: Nadine Gerlach 
> Date: Thu, 28 May 2020 at 14:21
> Subject: Refmac error
> To: 
>
>
> Hey everybody,
>
> I am running refmac in CCP4 ccloud after Coot and I get this error message:
>
>  *** error running refmac5: Error in command.call
> Return code: 512
>
> Any held is really appreaciated!
>
> Best wishes,
> Nadine
>
> --
> Nadine Gerlach
> PhD candidate
> MPG MARUM Bridge Group Marine Glycobiology
> MARUM, University Bremen & Max Planck Institute for Marine Microbiology
> Tel: +49 421 218-65758
> Email: nger­lach@mpi-bre­men.de, ngerl...@marum.de
> MARUM Pavillon room 1110
> Leobener Straße
> 28359 Bremen, Germany
>
> This email and any attachments are intended solely for the use of the
> named recipients. If you are not the intended recipient you must not use,
> disclose, copy or distribute this email or any of its attachments and
> should notify the sender immediately and delete this email from your
> system. UK Research and Innovation (UKRI) has taken every reasonable
> precaution to minimise risk of this email or any attachments containing
> viruses or malware but the recipient should carry out its own virus and
> malware checks before opening the attachments. UKRI does not accept any
> liability for any losses or damages which the recipient may sustain due to
> presence of any viruses. Opinions, conclusions or other information in this
> message and attachments that are not related directly to UKRI business are
> solely those of the author and do not represent the views of UKRI.
>
> --
> Nadine Gerlach
> PhD candidate
> MPG MARUM Bridge Group Marine Glycobiology
> MARUM, University Bremen & Max Planck Institute for Marine Microbiology
> Tel: +49 421 218-65758
> Email: nger­lach@mpi-bre­men.de, ngerl...@marum.de
> MARUM Pavillon room 1110
> Leobener Straße
> 28359 Bremen, Germany
>
>

This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 

[ccp4bb] Fwd: Re: What refinement programs are fully Open Source?

[Helen Ginn]

Hi Pietro!

As for free and open-source (GPLv3 license) refinement software, I am 
developing Vagabond.


https://vagabond.hginn.co.uk

It is based on refining bond torsion angles in an ensemble of related 
structures which also captures flexibility (no B factors!). There are no 
restraints, only constraints. This allows a significant side-step of the 
parametrisation problem and reduces the level of overfitting in the map 
(which is more widespread than I first realised).


It is in the middle of development, very young and therefore not as 
polished or refined as other (atomistic) refinement software, and is 
currently best used as an intermediate tool, when you have confusing and 
muddy electron density, to create a less overfitting-biased map to build 
into and then continue with your favourite other refinement software.


git clone https://www.github.com/helenginn/vagabond.git

Typing this into a command line will demonstrate how open source it is!

Helen

---

On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote:

Dear all,

we are in the editorial stages of a manuscript that I submitted to 
Wellcome Open Research for publication.


The journal/editor ask us to list fully Open Source alternatives to the 
pieces of software we used, for example for data processing and 
refinement.


What refinement programs are fully Open Source?

Thanks!

Pietro

Pietro Roversi




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Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Gihan Ketawala]

Guys, Thanks for all the help. I figured out what's wrong with the sequence 
file. 
I had accedently entered an "X' to one of the sub-chains.

Cheeres !
Gihan




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Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Michel Fodje]

In Ascoidea asiatica where CUG is translated as both Leu and Ser.
Mühlhausen S., Schmitt H.D., Pan K.T., Plessmann U., Urlaub H., Hurst L.D., 
Kollmar M. Endogenous stochastic decoding of the CUG codon by competing Ser- 
and Leu-tRNAs in Ascoidea asiatica. Curr. Biol. 2018; 28:2046-2057.

Perhaps, this is not a mutation at all but points to the origin of this virus.

/Michel.

From: CCP4 bulletin board  On Behalf Of Carter, Charlie
Sent: March 21, 2020 7:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19




Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structural biologist you won't be able to do much 
about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how fast we 
can get started.  There are 21 PDBs already and some even have bound ligands.  
Good job Frank et al. BTW!  And my personal thanks to all of you out there who 
are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on the 
structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
there are not that many proteins in it.  If all of us independently do the same 
bioinformatics and literature searches and end up trying exactly the same thing 
in every lab all over the world, then that would be more than unfortunate.  To 
that end, I am personally interested on ORF8 for reasons I will go into below.  
Has anyone tried to solve it yet?  What happened?  Didn't express? Bad 
diffraction?  What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and labs 
dark while we shelter-in-place.  That doesn't mean our hands are tied.  We are 
still allowed to think. The fraction of the human race that has a snowball's 
chance in Hades of figuring out this bug is very very small.  Structure may be 
your main skill set, but you are still a biologist.  Do you know how to run a 
PCR machine?  Do you know how to pipette?  You might think that anybody can do 
it, but that is really not the case. Ever trained a new student on sterile 
technique?  How many days did that take?  Now remember that your student was no 
dummy and already studying biology.  Everyone reading this will make an 
excellent volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we do, 
often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The void 
left by the dearth and delay of test results has been filled with fear, and 
that is a big problem.  The tests, as defined, are straightforward, but also 
extremely regimented like any good laboratory protocol should be.  The US CDC's 
instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for clinical but 
for academic use?  I think more than a few people on this list could be 
regarded as experts in making a complex biochemical task faster, more 
efficient, high-throughput and nonetheless valid.  Yes, there are other people 
who do virus testing for a living, but right now they are all rather busy.  
Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in this 
article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
will find what I'm talking about.  The authors found two "types" of SARS-CoV-2. 
 They call them "S" and "L" because the only conserved amino acid change 
involved is S84L in ORF8.  The "S" type is believed to be the ancestor of "L".  
What is interesting is how tightly linked this mutation is to a silent mutation 
on the other end of the genome: the "L" type has a faster codon for Ser in 
ORF1.  Such tight coupling (r^2=0.945) means there must be significant 
selective pressure preventing both of these mutations occurring in the same 
virus at the same time.  That, I believe, is

[ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Carter, Charlie]

Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structural biologist you won't be able to do much 
about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how fast we 
can get started.  There are 21 PDBs already and some even have bound ligands.  
Good job Frank et al. BTW!  And my personal thanks to all of you out there who 
are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on the 
structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
there are not that many proteins in it.  If all of us independently do the same 
bioinformatics and literature searches and end up trying exactly the same thing 
in every lab all over the world, then that would be more than unfortunate.  To 
that end, I am personally interested on ORF8 for reasons I will go into below.  
Has anyone tried to solve it yet?  What happened?  Didn't express? Bad 
diffraction?  What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and labs 
dark while we shelter-in-place.  That doesn't mean our hands are tied.  We are 
still allowed to think. The fraction of the human race that has a snowball's 
chance in Hades of figuring out this bug is very very small.  Structure may be 
your main skill set, but you are still a biologist.  Do you know how to run a 
PCR machine?  Do you know how to pipette?  You might think that anybody can do 
it, but that is really not the case. Ever trained a new student on sterile 
technique?  How many days did that take?  Now remember that your student was no 
dummy and already studying biology.  Everyone reading this will make an 
excellent volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we do, 
often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The void 
left by the dearth and delay of test results has been filled with fear, and 
that is a big problem.  The tests, as defined, are straightforward, but also 
extremely regimented like any good laboratory protocol should be.  The US CDC's 
instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for clinical but 
for academic use?  I think more than a few people on this list could be 
regarded as experts in making a complex biochemical task faster, more 
efficient, high-throughput and nonetheless valid.  Yes, there are other people 
who do virus testing for a living, but right now they are all rather busy.  
Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in this 
article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
will find what I'm talking about.  The authors found two "types" of SARS-CoV-2. 
 They call them "S" and "L" because the only conserved amino acid change 
involved is S84L in ORF8.  The "S" type is believed to be the ancestor of "L".  
What is interesting is how tightly linked this mutation is to a silent mutation 
on the other end of the genome: the "L" type has a faster codon for Ser in 
ORF1.  Such tight coupling (r^2=0.945) means there must be significant 
selective pressure preventing both of these mutations occurring in the same 
virus at the same time.  That, I believe, is interesting.  Espeically since 
they are so far apart I expect this selective pressure might work in trans: as 
in a super-infection. That is, the S and L genome types may interfere with each 
other.

The authors fall short of claiming evidence of interference upon 
super-infection, and indeed they have already been criticised for calling "L" 
the "aggressive" type.  But it is still interesting and points a finger at ORF8.

ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a stretch of 
60 residues.  This homologous region contains the S84L site (Val I544 in 5o32). 
 I had a quick look and appears to be a cavity-filling mutation 

[ccp4bb] Fwd: [ccp4bb] Fw: protein protein interactions

[RUBEN SANCHEZ GARCIA]

Dear Careina,

I would recommend you our partner-specific binding site predictor:  
BIPSPI, that uses as input 2 sequences or 2 pdb files and proposes the  
binding site of the two partners.


http://bipspi.cnb.csic.es/xgbPredApp/

Kind regards,

Ruben


Quoting "careinaedgo...@yahoo.com"  
<02531c126adf-dmarc-requ...@jiscmail.ac.uk>:


Dear allApologies for off topic question but can anyone recommend  
good programs for identifying docking interfaces between two  
proteins. I do not know that these two proteins interact. I would  
like a level of confidence on a possible interaction. is there a  
good program to do this?kind regardsCareina




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- End forwarded message -




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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
--- Begin Message ---

Dear Careina,

I would recommend you our partner-specific binding site predictor:  
BIPSPI, that uses as input 2 sequences or 2 pdb files and proposes the  
binding site of the two partners.


http://bipspi.cnb.csic.es/xgbPredApp/

Kind regards,

Ruben


Quoting "careinaedgo...@yahoo.com"  
<02531c126adf-dmarc-requ...@jiscmail.ac.uk>:


Dear allApologies for off topic question but can anyone recommend  
good programs for identifying docking interfaces between two  
proteins. I do not know that these two proteins interact. I would  
like a level of confidence on a possible interaction. is there a  
good program to do this?kind regardsCareina




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--- End Message ---

[ccp4bb] Fwd: Open scientist position at the EMBL-Grenoble - Project leader for ID30A/MASSIF-1 beamline upgrade

[Andrew MC CARTHY]

 

Dear all, 

Just a quick reminder that the closing date for applications is in one
week (Feb 7th). 

We have an open scientist position at the EMBL-Grenoble for a Project
leader to oversee our contribution to the upgrade of the fully automated
ID30A/MASSIF-1 macromolecular crystallography beamline at the ESRF. This
is an exciting opportunity for an ambitous individual to join a team of
scientists and engineers from the EMBL and ESRF in developing fully
automated data collection protocols to maximise the scientidic potential
of the ESRF Extremely Brilliant Source upgrade. 

Closing date: Feb. 7th 2020. 

Interview date: March 6th, 2020 

You can read more about the position and submit your application at: 

https://www.embl.de/jobs/searchjobs/index.php?ref=GR00139 

Best regards, 

Andrew



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Re: [ccp4bb] Fwd: [ccp4bb] suggestions on small proteins that for a complex

[Artem Evdokimov]

FliS and FliC

Artem

On Sun, Nov 10, 2019, 03:42 Gianluca Cioci  wrote:

> ps: the 3D structure
>   of the complex should
> be solved at high resolution
>
> ;o)
>
>
>
>
> Dear All,
>
> I am looking for examples of two small proteins A and B that can form a
> tight complex AB.
> Each protein should be straightforward to express in E.coli, well folded
> and stable in the isolated form.
> Also, if possible, I would prefer monomeric proteins (although not
> really mandatory).
> Is anybody able to give me some suggestions ?
>
> Thank you,
>
> GIA
>
> --
> 1st French Congress on Integrative Structural Biology
> Please check: http://bsi-2019.ipbs.fr
>
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute (TBI)
> BioCatalysis Team
>
> http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulouse
> http://cribligand.ipbs.fr/index.html
>
> Tel: +33 (0)5 61 55 97 68
> E-mail: ci...@insa-toulouse.fr
>
> TBI - INSA Toulouse
> 135 avenue de Rangueil
> 31077 Toulouse CEDEX 04
> http://www.toulouse-biotechnology-institute.fr
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Fwd: [ccp4bb] suggestions on small proteins that for a complex

[Gianluca Cioci]

ps: the 3D structure
 of the complex should
be solved at high resolution

;o)




Dear All,

I am looking for examples of two small proteins A and B that can form a
tight complex AB.
Each protein should be straightforward to express in E.coli, well folded
and stable in the isolated form.
Also, if possible, I would prefer monomeric proteins (although not
really mandatory).
Is anybody able to give me some suggestions ?

Thank you,

GIA

--
1st French Congress on Integrative Structural Biology
Please check: http://bsi-2019.ipbs.fr

Dr. Gianluca CIOCI
Toulouse Biotechnology Institute (TBI)
BioCatalysis Team
http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
PICT - Plateforme Intégrée de Criblage de Toulouse
http://cribligand.ipbs.fr/index.html

Tel: +33 (0)5 61 55 97 68
E-mail: ci...@insa-toulouse.fr

TBI - INSA Toulouse
135 avenue de Rangueil
31077 Toulouse CEDEX 04
http://www.toulouse-biotechnology-institute.fr



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[ccp4bb] Fwd: CCP4i2 London Road Show

[Nicholas Keep]

Reminder One week to London CCP4i2 Road show.  Places still available.

*CCP4 i2 Road Show, London*

There will be a CCP4 Road Show for use of the i2 interface on Tuesday 
12th November, at Birkbeck College.
*Time:* 14:00 - 16:00 for the main workshop with about an hour 
afterwards for those with additional questions.

*Place:* Room 416 in the main Birkbeck Malet St Building.
There will be 2-3 CCP4 tutors presenting the Road Show.
While it is primarily intended for the extensive number of 
crystallographers in London, all are welcome.
There will be places for 40 participants. Desktops will be used, but you 
are also welcome to use your laptops (but if doing so please ensure 
you install the software in advance - see CCP4 webpages for guidance on 
how to do this).


To book a place on a first come first served basis please register at 
http://www.bbk.ac.uk/booking/event/8829


Event page is http://www.bbk.ac.uk/events/remote_event_view?id=8829

Best wishes

Nick Keep and Keith Wilson

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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[ccp4bb] Fwd: [Labmanagers] CCP4i2 London Road Show

[Nicholas Keep]

Reminder Two weeks to London CCP4i2 Road show.  Places still available.

*CCP4 i2 Road Show, London*

There will be a CCP4 Road Show for use of the i2 interface on Tuesday 
12th November, at Birkbeck College.
*Time:* 14:00 - 16:00 for the main workshop with about an hour 
afterwards for those with additional questions.

*Place:* Room 416 in the main Birkbeck Malet St Building.
There will be 2-3 CCP4 tutors presenting the Road Show.
While it is primarily intended for the extensive number of 
crystallographers in London, all are welcome.
There will be places for 40 participants. Desktops will be used, but you 
are also welcome to use your laptops (but if doing so please ensure 
you install the software in advance - see CCP4 webpages for guidance on 
how to do this).


To book a place on a first come first served basis please register at 
http://www.bbk.ac.uk/booking/event/8829


Event page is http://www.bbk.ac.uk/events/remote_event_view?id=8829

Best wishes

Nick Keep and Keith Wilson

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door




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[ccp4bb] Fwd: Retinal Proteins Conferences - Historical Website

[Schertler Gebhard (PSI)]

Prof. Gebhard F.X. Schertler
Structural Biology ETH Zürich D-BIOL

Head of Biology and Chemistry
Division
Paul Scherrer Institut
Laboratory of Biomolecular Research,
LBR
OFLC 109
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265

Anfang der weitergeleiteten Nachricht:

Von: Leonid Brown mailto:lebr...@uoguelph.ca>>
Datum: 28. September 2019 um 04:34:11 MESZ
An: Undisclosed recipients:;
Betreff: Retinal Proteins Conferences - Historical Website

Dear colleagues,

I am happy to announce that we launched a historical website dedicated to past 
ICRPs (International Conferences on Retinal Proteins), at 
http://icrp2018.retinalproteins.org/. I want to thank everyone who provided the 
historical materials and Rob Reedijk (University of Toronto) for his work on 
the website design.

As you will see from perusing the site, it is a beta version and some pages are 
incomplete. So I encourage you to send any materials you will find missing from 
those pages, especially on some of the older conferences.

Thank you in advance for your support. Feel free to send the link to anyone who 
may be interested.

Best regards Leonid


Leonid S. Brown, Ph.D.
Professor, Department of Physics,
Associate Dean of Research and Graduate Studies, CEPS,

University of Guelph, Ontario N1G 2W1, Canada
phone, voice mail: 519-824-4120 x53295 or x53777
https://www.physics.uoguelph.ca/people/leonid-s-brown
email: lebr...@uoguelph.ca




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[ccp4bb] Fwd: [3dem] Postdoctoral Position at NNF-CPR University of Copenhagen

[Guillermo Montoya]

Dear Colleagues

just a kindly reminder,  the application deadline is the 18th August,

Those interested, please apply through the link provided below

 
https://candidate.hr-manager.net/ApplicationInit.aspx/?cid=1307=18997=149912=5=false


Best regards


G.





Dear colleagues,
We are seeking an excellent and highly motivated postdoctoral candidate to lead 
a project combining biochemistry, SPA cryoEM and crystallography to study 
protein-DNA complexes that allow the insertion of large DNA segments into a 
genome. The position is funded through an NNF distinguished investigator grant. 
The ideal candidate for this project will be a structural biologist with 
experience in protein-DNA biochemistry and cryoEM and/or crystallography 
expertise. The position is funded for 3 years (2+1) with a possible extension 
for a 4th year. For informal inquiries you can contact me or Lotta Avesson (in 
cc).
Our institute provides the state-of-the art infrastructure and instrumentation 
including a Titan Krios  TEM equipped with the state-of-the-art direct electron 
detector and 3 auxiliary TEMs for sample characterisation. We expect to 
incorporate another 200 Kv system with a DED camera by the end of the year. In 
addition, the selected person will benefit from an intellectually stimulating, 
supportive and collaborative environment, including access to soft skills 
workshops run by our center and the University of Copenhagen (project writing 
courses, career development and  leadership workshops), and a range of enabling 
core facilities in the centre including crystallisation, protein production, 
molecular biophysics, high performance computing, bioinformatics, and mass 
spectrometry.

best regards


G.

Guillermo Montoya, Prof., Dr.
Research Director, Protein Structure and Function Programme
Novo Nordisk Foundation Center for Protein Research
Faculty of Health and Medical Sciences, University of Copenhagen,
Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
web: www.cpr.ku.dk
PC: Lotta Avesson lotta.aves...@cpr.ku.dk
___




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[ccp4bb] Fwd: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound to Zn2+

[Daniel M. Himmel, Ph. D.]

-- Forwarded message -
From: Daniel M. Himmel, Ph. D. 
Date: Mon, Aug 5, 2019 at 12:45 PM
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Extra density close to
phosphate bound to Zn2+
To: 


Pentagonal phosphate geometry would be a transition state, except that
three oxygens
would be more or less co-planar.  Would anything approaching a transition
state show up in the electron
density of a crystal structure?  In myosin ATPase structures, there are
phosphate analogs with geometry
that approximates a transition state.

-Daniel


On Mon, Aug 5, 2019 at 11:55 AM  wrote:

> Hi Maria,
>
>
>
> Did you rotate the phosphate, or invert it? If you invert the phosphate,
> you may get into trouble with the parameters. Although a phosphate is
> symmetric, its oxygens have different names and inverting it leads to all
> kind of problems, especially in a high resolution map which does not allow
> the phosphate to flip it back in an “allowed” conformation.
>
>
>
> If you did rotate the phosphate, I take my words back and you may have to
> look for ions.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Maria Håkansson
> *Gesendet:* Montag, 5. August 2019 17:32
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Extra density close to phosphate bound
> to Zn2+
>
>
>
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>
>
>
> Hi,
>
>
>
> Thanks for your suggestions but I have tried to invert the phosphate and
> it is not
>
> fitting the map. The geometry is not correct that way and it is too good
> data to ignore and
>
> to my knowledge a pentacoordinated phosphate is a non existent species.
>
>
>
> That leaves me with ions.
>
>
>
> Best regards,
>
> Maria
>
>
>
>
>
> Maria Håkansson, PhD, Crystallization Facility Manager
> Principal Scientist
>
> SARomics Biostructures AB
> Medicon Village
> SE-223 81 Lund, Sweden
>
> Mobile: +46 (0)76 8585706
> Web: www.saromics.com
> 
>
>
>
>
>
>
>
>
>
> On 5 Aug 2019, at 16:32, Jan Abendroth  wrote:
>
>
>
> Hi Maria,
>
> apart from the suggestions that were already made, take a look at the P-O
> bond on the right side of the P. Maybe it is just the perspective, this
> appears to be rather long.
>
> So, instead of the alternate conformation, maybe just a flip of the
> phosphate and a water off to the right?
>
>
>
> Cheers,
>
> Jan
>
>
>
> On Mon, Aug 5, 2019 at 7:16 AM Nukri Sanishvili 
> wrote:
>
> Hi Maria,
>
> Let's not ignore the "missing" density - the red one. If the question is
> only P vs S, a sulfur would add to the negative density, i.e. make matters
> worse. It also appears that modeling a phosphate in alternative
> conformations, as suggested by Wim and Roger, would take care of the issue
> of negative density as well.
>
> Cheers,
>
> Nukri
>
>
>
> On Mon, Aug 5, 2019 at 8:05 AM Maria Håkansson <
> maria.hakans...@saromics.com> wrote:
>
> Dear CCP4 bulletin board,
>
>
>
> I am working with some lytic enzymes called endolysines, which
>
> bind Zn2+ in the active site. I have three homologues protein
>
> determined to 1.2 Å each where the Zn2+ is bound
>
> to a cystein, two histidines and one phosphate ion added (1.9-2.3 Å
> binding distances) in the crystallization experiment.
>
>
>
> Now to my question. Close to the phosphate (B-factor=20Å2) ion a 8 sigma
> peak is present in all three endolysines, see below.
>
> I have modeled it to a Na+ (B-factor= 30 Å2) or a Li+ (B factor = 13Å2)
> ion.
>
> Sodium has benn added in the crystallization experiments since sodium
> potassium phosphate
>
> salt has been used. The only reason for including Li+ is that I think the
> binding distances (1.7-2.0 Å) are too short for Na+.
>
>
>
> I have also tried to make a model with the phosphate in two different
> conformations but it does not fit.
>
>
>
> Have anyone seen something similar before? What is the most correct way of
> dealing with unknown densities?
>
> It is difficult to disregard +8 sigma difference density close to the
> active site.
>
>
>
> Thanks in advance for any help!
>
>
>
> Best regards,
>
> Maria
>
>
>
>   ion.png>
>
>
>
> Maria Håkansson, PhD, Crystallization Facility Manager
> Principal Scientist
>
> SARomics Biostructures AB
> Medicon Village
> SE-223 81 Lund, Sweden
>
> Mobile: +46 (0)76 8585706
> Web: www.saromics.com
> 
>
>
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> 

[ccp4bb] Fwd: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[Carter, Charlie]

Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2
Date: July 19, 2019 at 1:32:53 PM EDT
To: Patrick Loll mailto:pjl...@gmail.com>>

Hi Pat,

I, too have fallen into this rabbit hole while Mark Rould and I were writing a 
Methods in Enzymology chapter on Fobs - Fobs difference Fourier maps as a 
vastly better tool for documenting ligands. Mark had documented a similar 
offense, and I had previously also encountered one. Both cases occurred since 
structure factor deposition was frequent and/or required, so it was relatively 
trivial to do the definitive experiments. The density of outright fraudulent 
results of this type in high profile journals long ago persuaded me that unless 
someone pointed me to an especially salient article, that those journals did 
not merit my attention, and I’ve several times refused to review manuscripts 
for them, for much the same reason.

I was recently asked to teach a module on scientific fraud in a newly required 
course on ethics for NIH Programmatic grants. It was both amusing and 
rewarding, as the students readily understood many of these issues.

“Scholarly Publishing” is something best left to professional societies in my 
(admittedly extreme) opinion.

Charlie

On Jul 19, 2019, at 1:17 PM, Patrick Loll 
mailto:pjl...@gmail.com>> wrote:

The idea of contacting the editor (and/or author) is an excellent one, and 
indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve 
been down this path before with a high-profile vanity journal, and while the 
editors paid lip service to the notion that the record should be corrected, in 
reality they led me on for the better part of a year, and got me to write up 
detailed analyses of why the ligand positioning was not justified, before 
eventually saying “no, we don’t see any need to publish a correction.” I 
speculate that the journal prefers not avoid corrections, for fear that too 
many corrections will make the journal a less desirable destination.

On 19 Jul 2019, at 11:23 AM, Bärbel Blaum 
mailto:baerbel.bl...@intherabio.com>> wrote:

Hi Rhys,
the reported B-factors for the “ligands” are all way below the reported 
B-factors for the protein chains, with the worst of the three complexes 
reporting unitless numbers 23.2 and 64.8, respectively, just to highlight *one* 
striking feature of the data collection and refinement table. So even with the 
limited info normally available to reviewers this table should have raised a 
red flag. After the re-refinement suggested by others, i.e. your own proper 
assessment of the crystallographic data, if you do not find noteworthy density 
you may want to contact the article’s editor with your results. If you work in 
this field, i.e. really care about this paper scientifically and you are not 
afraid to confront the authors you could suggest writing a comment/direct 
response article but in my opinion that would only make sense if you can be 
sure beforehand that it will be linked visibly to the actual paper, else it 
will be a waste of time. And don’t forget that just because one or some of the 
authors did a bad job at the crystallographic end other findings of the paper 
might still be solid – in collaborations often one author is unable to 
critically evaluate another author’s contribution and this would not be the 
first case were good synthetic or biological work is presented along with a bad 
crystal structure.
By the way and a bit ironically this protein may have suffered bad 
crystallography/scientific practice before - I think it was one of the fake 
Krishna Murthy structures, right? The associated (now retracted) article I mean 
is here
https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub
Kind regards, Bärbel
---
Bärbel Blaum, PhD
Inthera Bioscience AG
Einsiedlerstrasse 34
CH-8820 Waedenswil
Switzerland
E-Mail: baerbel.bl...@intherabio.com
Phone: +41 43 477 94 72--



Von: CCP4 bulletin board  im Auftrag von "Manfred S. 
Weiss" 
Antworten an: "Manfred S. Weiss" 
Datum: Freitag, 19. Juli 2019 um 16:03
An: 
Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

Hi Rhys,

all three structures are at modest resolution and they don't seem to
be properly refined. At least they are all below average. I wonder
how this paper made it past the referees.

I haven't checked the paper, but there are ways and means how to
deal with weakly bound ligands in the best possible way. One aspect
is to improve the phases as much as possible without having the ligand
present. This was obviously NOT done. Another way is to use the
PANDDA approach, which relies on having many data sets available.
I suppose that this was also not done.

The best way to check is to delete the ligand and so some extensive
refinement in order to remove the phase bias introduced by the
ligand. Only then you can reliably assess whether something is there
or 

[ccp4bb] Fwd: [ccp4bb] AKTA FPLC fractionation peak by peak

[Sorin Draga]

Thank you both for your answers!

*Upasana* - the chromatogram was randomly selected to ilustrate the point -
we do a careful equilibration of the column and degas the mobile phase(s)
before starting. I'm not really sure what you mean by oligomeric state of
the protein - we are working with complex proteic mixtures that are not
characterized, hence the need for fractionation.
*Matthias* - your advice is spot on! I will give it a try and keep you
posted.


On Mon, Jun 3, 2019 at 10:24 AM Barone, Matthias 
wrote:

> Hi sorin
> The problem in your elution profile is that you cannot define a global
> threshold as the baseline is heavily bent (relative to the peak heights)
> and starting to fractionate at 6' is not the problem, telling the script to
> stop once you reach baseline at 13' is.
> I would try what you proposed: Given that your peak elution time points
> are reproducible, I'd actually work with the "watch" function and turn it
> on while watching OD for the given time windows.  fractionate the first
> block when OD exceeded a certain threshold and then turn the watch function
> off after, say 13'. Turn it back on at 20' and fractionate into another
> well. Use the time as base and keep the Äkta pumping at constant speed.
> Curious if someone knows a better strategy!
> Best, matthias
>
> --
> *From:* CCP4 bulletin board  on behalf of Sorin
> Draga 
> *Sent:* Monday, June 3, 2019 8:29:40 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] AKTA FPLC fractionation peak by peak
>
> Dear all,
>
> We have an old akta system, running Unicorn 4.0, recently donated to our
> lab. While attempting to fractionate a protein mixture, I was unable to
> convince Unicorn to fractionate within given limits (say, for ex peak A
> between RT a and b and peak B between retention times c and d). All that I
> could manage to do is fractionate at a fixed time interval.
> For clarity, I have attached a picture below (orange square would be what
> we actually want to fractionate)
> Any help would be appreciated, as we are pressed for time ( I am certain
> that we are missing something simple)
>
> Thank you!
> [image: image.png]
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Fwd: Domainex is hiring a Structural Biologist

[Mark Roe]

Posted on behalf of Domainex.




Begin forwarded message:

From: Stefanie Reich mailto:s.re...@domainex.co.uk>>
Date: 31. May 2019 at 17:04:20 CEST
To: "ccp4bb@jiscmail.ac.uk" 
mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Domainex is hiring a Structural Biologist


https://www.domainex.co.uk/about-us/recruitment#3

  *



Domainex has a full-time permanent vacancy in our Protein Science Team, which 
offers our clients a comprehensive range of services including molecular 
biology, protein production for assays and structural biology, and structural 
analysis of proteins by X-ray crystallography.  Our unique, patented, 
Combinatorial Domain Hunting technology allows us to make and work with 
proteins that are otherwise refractory to recombinant expression.

All applicants must be able to solve X-ray crystal structures independently and 
have a good working knowledge of the current software packages employed in 
protein crystallography (esp. XDS, CCP4, coot). They should be able to 
demonstrate postdoctoral level experience of solving structures of 
protein-ligand complexes over a range of target classes in a drug discovery 
environment, experience in the use of biophysical techniques would be a 
significant plus. Candidates must also have expertise in molecular biology; 
recombinant protein expression and purification in E. coli, insect or mammalian 
cells; and substantial experience of using AKTA chromatography equipment (or 
similar) for protein purification to X-ray crystallography standard.

This role requires the ability to plan and implement experimental programmes, 
to solve any problems that arise, and to work effectively within project teams 
to deliver high-quality results to our clients. Laboratory work is a major 
element of this varied and challenging role.  Essential attributes include 
diligent reporting of results, data interpretation, and an ability to make 
recommendations for further studies. It will also be necessary to communicate 
your results effectively to our clients.



Job requirements:

PhD with track-record of relevant and proven experience, i.e. publications and 
PDB depositions.

Independence and team working; flexibility to take on different projects; 
ability to make a meaningful impact on clients.

Ability to work on your own initiative, and to consistently deliver high 
quality results.

Creative thinking coupled to delivery of novel outcomes that leads to 
opportunities for inventorship or publications (papers/research articles).



To apply for this role, please send your CV and a covering letter, quoting 
reference PS0519, to 
recruitment2...@domainex.co.uk.







Email confidentiality notice: This message is private and confidential. If you 
have received this message in error, please notify us and remove it from your 
system. Domainex Ltd is registered in England and Wales. Company No. 04336899. 
Registered office: Chesterford Research Park, Little Chesterford, Saffron 
Walden, Essex, CB10 1XL, UK.




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[ccp4bb] Fwd: Open PhD position UiO Protein Biochemistry

[Ute Krengel]

Forwarded on behalf of Sandip Kanse, University of Oslo:


 Forwarded Message 
Subject: Open PhD position UiO Protein Biochemistry
Date: Fri, 26 Apr 2019 08:52:06 +0200
From: Sandip Kanse 
To: Ute Krengel 

PHD RESEARCH FELLOW IN PROTEIN BIOCHEMISTRY
UNIVERSITY OF OSLO, NORWAY.

Applications are invited for a 3-4 year position for a Research 
Fellowship as a PhD Candidate in protein biochemistry to be based in the 
Vascular Pathophysiology Lab (Head: Prof. Sandip Kanse) in the Faculty 
of Medicine, Institute of Basic Medical Sciences, Department of 
Molecular Medicine at the University of Oslo.  This group focusses on 
understanding the role of proteases in cardiovascular diseases such as 
thrombosis and stroke using biochemical, cellular and molecular 
techniques and in vivo mouse models.
The candidate will work on a project that is related to the structural 
analysis of proteases in blood using x-ray crystallography and 
cryo-electron microscopy. The main activities will consist of expression 
recombinant proteins and their purification, designing and expressing 
mutants and testing them in relevant assays. Finally, performing screens 
that will lead to the determination of protein structures using x-ray 
crystallography or cryo-electron microscopy. The aim is to understand 
activation and inhibition mechanisms of proteases at an atomic level. 
The project will be done in collaboration with the Oslo Structure 
Biology group 
https://www.mn.uio.no/ibv/english/research/groups/px/index.html.

Contact information
Professor Sandip Kanse, e-mail: sandip.ka...@medisin.uio.no, Tel: 
+47-22851464
Lab Web pages: 
https://www.med.uio.no/imb/english/research/groups/vascular-patho-physiology/index.html

Complete advertisement and link to application portal
https://www.jobbnorge.no/ledige-stillinger/stilling/168641



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[ccp4bb] Fwd: SFX beamline scientist position at the SwissFEL

[Wang Meitian (PSI)]

Somehow the link changed, here is the updated one.

https://www.psi.ch/en/pa/job-opportunities/27905-beamline-scientist

Best
meitian

Begin forwarded message:

From: Meitian Wang mailto:meitian.w...@psi.ch>>
Subject: SFX beamline scientist position at the SwissFEL
Date: 18 April 2019 at 10:32:01 CEST
To: "CCP4BB@jiscmail.ac.uk" 
mailto:CCP4BB@JISCMAIL.AC.UK>>

Dear all,

I would like to draw your attention to a tenure-track beamline scientist 
position in macromolecular crystallography group at the Photon Science 
Division, Paul Scherrer Institut 
(https://www.psi.ch/macromolecular-crystallography/). This position offers a 
unique opportunity to develop and operate a dedicated serial femtosecond 
crystallography (SFX) station at the SwissFEL. Detailed information and the 
online application portal can be found at 
https://www.psi.ch/pa/stellenangebote/2000.

Best regards,
meitian

__
Meitian Wang
Head of Macromolecular Crystallography Group
Photon Science Division
Paul Scherrer Institut
+41 56 310-4175





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Re: [ccp4bb] Fwd: [ccp4bb] SO4 or PO4

[Jan Stransky]

This can be done at Diamond I23 beamline.

https://doi.org/10.1016/j.nimb.2016.12.005

Best regards,

Jan

Dne 16.02.2019 v 18:49 Patrick Loll napsal(a):
> S has about 0.56 anomalous electrons at 8 keV, whereas P has about
> 0.44. This is a small difference between two weak signals—unlikely to
> give a clear result. If you could get to the sulfur & phosphorus
> edges, then you could (in principle) answer this, but that’s a very
> hard experiment to accomplish.
>
>
>> Begin forwarded message:
>>
>> *From: *jlliu20022002 liu > >
>> *Subject: **Re: [ccp4bb] SO4 or PO4*
>> *Date: *February 16, 2019 at 11:14:07 AM EST
>> *To: *CCP4BB@JISCMAIL.AC.UK 
>> *Reply-To: *jlliu20022002 liu > >
>>
>> How about collect data at sulfur peak. You might see anomalous peak
>> for sulfur.
>>
>> Jinyu
>>
>> On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn
>> > wrote:
>>
>> Dear all
>>
>> I have got a crystal grown at the condition both have ion of SO4
>> and PO4, and the diffraction resolution is very well, but the
>> problem is coming: how to tell which is which just from electron
>> density? I think they are exactly same. Thanks a lot !!!
>>
>> Beat Regards
>>
>> Shijun
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> ---
>
> Patrick J. Loll, Ph. D.  
>
> Professor of Biochemistry & Molecular Biology
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pjl...@gmail.com 
>
> pj...@drexel.edu 
>
>
>
> 
>
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>



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[ccp4bb] Fwd: [ccp4bb] SO4 or PO4

[Patrick Loll]

S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44. This 
is a small difference between two weak signals—unlikely to give a clear result. 
If you could get to the sulfur & phosphorus edges, then you could (in 
principle) answer this, but that’s a very hard experiment to accomplish.


> Begin forwarded message:
> 
> From: jlliu20022002 liu 
> Subject: Re: [ccp4bb] SO4 or PO4
> Date: February 16, 2019 at 11:14:07 AM EST
> To: CCP4BB@JISCMAIL.AC.UK
> Reply-To: jlliu20022002 liu 
> 
> How about collect data at sulfur peak. You might see anomalous peak for 
> sulfur.
> 
> Jinyu
> 
> On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn 
> > wrote:
> Dear all
> 
> I have got a crystal grown at the condition both have ion of SO4 and PO4, and 
> the diffraction resolution is very well, but the problem is coming: how to 
> tell which is which just from electron density? I think they are exactly 
> same. Thanks a lot !!!
> 
> Beat Regards
> 
> Shijun
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 
---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu




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[ccp4bb] Fwd: Head of Membrane Protein Science opportunity available at fast-growing biotech company

[Pius Padayatti]

Forwarding a job advertisement
Please contact the person here copied
Lorin
-- Forwarded message -
From: Lorin Raats 
Date: Tue, Feb 12, 2019 at 6:53 AM
Subject: Head of Membrane Protein Science opportunity available at
fast-growing biotech company


It would be great to get in touch as I have a pretty interesting
opportunity available as Head of Membrane Protein Science for a small
innovative Drug Discovery company. Their novel technology allows for
discovery of chemically very diverse targets, with a high hit rate and
delivers more optimal compounds than the standard approaches. They have set
themselves the challenge to discover and develop compounds for unmet needs
in the fields of rare diseases, fibrosis, metabolic and various others.

As Head of the Protein Science group, you will play a key role in the
future success of the company. You will be able to set out the strategy and
align all the research activities, find new applications for the technology
platform and will report directly to the Board. Being a key factor in the
success of the company, this group will grow in size along with the company
and is expected to play an even bigger role in the future.

Does this sound like an interesting opportunity to you? Than let us get in
contact.

For now, enjoy the rest of the day!

Kind regards,


*Lorin Raats*
*Senior Associate R | Biotechnology *
Because we believe it is very important to share knowledge, information and
interests, we started bringing people together within the biotechnology
industry by creating an online community: www.biotechnologycommunity.com
[image: Logo]


Biotech/Pharma
Weerenweg 13 F
1161AE ZWANENBURG
the Netherlands

Tel:   +31(0)23-7548660
Mob: +31(0)6-30238143
Mail: l.ra...@qtcrecruitment.com
Web: www.qtcrecruitment.com
[image: linkedin]  [image:
xing]  [image:
viadeo]  [image: twitter]
 [image: myskype] [image: facebook]
 [image: youtube]



Please consider the environment before printing this email



-- 
P



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[ccp4bb] Fwd: Re: [ccp4bb] off-screen display window - problem solved

[Gerlind Sulzenbacher]

Dear all,

a big thanks, especially for the suggestions from Stuart, Phil and Huw.

I could solve the problem, but  working it the other way around:

the option "Displays have separate spaces" on my computer was off. I 
turned it on, logged out, no result, turned it off, logged out again, 
and now the windows appear on my screen. Well, the logic behind is not 
very clear, but at least I know what to do next time it happens,


I wish you all a nice day,

Gerlind



 Forwarded Message 
Subject:Re: [ccp4bb] off-screen display window
Date:   Tue, 12 Feb 2019 11:29:24 +
From:   Stuart McNicholas 
To: Gerlind Sulzenbacher 



Dear Gerlind,
  With thanks to Phil Evans and Huw Jenkins there are a couple of 
suggestions that I've seen passed around:


Phil found this on Stack Exchange:
"I met this problem before and it's very annoying. Finally, I realized 
that because the size and resolution of additional monitor are different 
from my Mac's. Those resulted in a 'non-existing' space between 
monitors. Sometimes windows would locate in that space and could not be 
moved. Luckily, I found we can remove the 'non-existing' space by 
changing settings on Mac. " System Preferences->Mission Control and 
uncheckDisplays have separate spaces." Then re-login MAC, the problem 
should be gone."


Huw had success with:
"I tried that first (as I knew about that one) but it didn't fix it as 
X11 Full-screen mode was also on. Turning off 'Displays have separate 
spaces' and Full-screen mode seemed to result in normal behaviour..."


Others may know a more definitive solution.

Best wishes,
Stuart


On Tue, 12 Feb 2019 at 11:24, Gerlind Sulzenbacher 
> wrote:


   Dear members of the community,

   when I launch ccp4i or Coot on my macbook OSMojave, the graphical
   window
   goes off-screen. I had the problem before and it went away by
   connecting
   to a new display screen - of course I was pleased about it, but yet I
   could not understand the logic behind this behaviour. The problem came
   back when I connected my Macbook to a videoprojector, and since then I
   do not find a solution. Re-installation of ccp4 and coot did not help.
   Has anybody encountered the same problem and found a way around?

   Thanks in advance for your advice,

   Gerlind

   -- 
   Gerlind Sulzenbacher

   Architecture et Fonction des Macromolécules Biologiques
   UMR7257 CNRS, Aix-Marseille Université
   Case 932
   163 Avenue de Luminy
   13288 Marseille cedex 9
   France
   Tel +33 491 82 55 66
   Fax +33 491 26 67 20
   E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr
   

   

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Re: [ccp4bb] Fwd: dry Shipper made in China

[Georg Mlynek]

If you buy a used one, or the one from Biobase China make a quality 
check before. Loosing crystals during shipment means loosing money 
(accounting for all the efforts that went in producing the crystals).


 I once got a protocol from Terese Bergfors at Uppsala University". It 
consists of what Taylor Wharton recommends (posted on diamond webpage), 
but some parts can't be found on their webpage.


*Care of dry shippers***updated July 2015/tex**

*Good Practices*

For optimal transportation of your crystals it is imperative that you 
look after your dry shipping dewars. Here are some tips on how to make 
sure that you don't lose your crystals or introduce ice onto your pucks 
and pins.


*Handling and loading*

·Handle with care. Sudden impact can damage the dewar: please ship your 
dewars in the appropriate shipping container.


·Be careful when placing heavy items (puck holders for example) in the 
dewar. Do not drop them in, since this could damage the neck of the dewar.


·Do not pack items that are too tall for the dewar, nor incorrectly 
install its lid to make the items fit. Forcing the lid down can damage 
the neck.


*Charging with liquid nitrogen*

·Charge the dewar as recommended in the manufacturer's instructions 
(photocopy these and tape to the side of the dewar if necessary).


·Minimise liquid nitrogen spillage on the vacuum release valve near the 
top of the dewar.


·Check that the 'charged' dewar weight is in line with manufacturer's 
recommendations E.g., in the case of the Taylor Wharton *CX-100* dry 
shipper dewar, it will weigh 3.6kg more than the 'dry' weight, and thus 
provide enough absorbed liquid nitrogen to keep the dewar at liquid 
nitrogen temperatures for 22days (16 days for the *CXR-100; *see 
overleaf for details*),* and only when brand new, and provided the 
vacuum has not been compromised.


·How do I check the dewar holds its charge? Do a NER (normal evaporation 
rate) test:


oRecord the tare weight (= the empty dewar plus its lid).

oProperly charge the dewar as per manufacturer's instructions, i.e. fill 
with liquid nitrogen and leave the dewar for 2-3 hours.


oExcessive accumulation of condensation or ice indicates damage.

oPour off the excess LN2. Record the drained weight = charged weight. 
Should be ≈3.6 kg more than the dry weight. Per the specs of a new 
CXR100, the absorbed amount of LN2 is approx. 3.7 liters of LN2. Once 
you see that number start going down, it is time to change the socks 
(usually every 3 years).


oAfter 24 hours, weigh it.

oRepeat again after 24 hours=48 hours total.

oThe maximum acceptable NER (normal evaporation rate) is 0.14 kg per 24 
hours.


·Check the dewar every time you use it (or at least every 3 months).

*Drying*

·Ensure the dewar is dried between uses. Residual moisture can cause 
damage to the foam material if frozen in situ.


·How do I speed up drying? What is the most effective procedure?

oPurge with dry nitrogen or air.

oLeave in a dehumidified room.

oIt is okay to use a boot drier (e-mail correspondence with 
Taylor-Wharton 2015.07/tex)


oBe careful: it may still take several days to fully dry.

·How do I know if it is dry?

oWeigh the dewar at time of purchase (record this on the dewar).

oWhen dry, the dewar should be within 0.5kg of the original dry weight.

oWeigh during drying until it no longer decreases.

·If you don't have time to dry the dewar properly between visits to 
synchrotrons, we strongly advise you to purchase more shipping dewars.


A well cared for dewar that is properly charged with liquid nitrogen 
before use should keep crystals safe for at least a week without 
refilling being required.


*What is the difference between CX100 and CXR-100?*

1. CXR100 vs. CX100

They are the same price here, so is one better than the other? The only 
difference I see is that one has a sock and one does not. Does the sock 
make the CXR100 a better dewar? (Better=holds temperature longer). No – 
Both units have socks inside of them. The CXR model allows you to 
replace the socks over time. The CX model the absorbent sock is 
permanently built into the unit, you can’t replace it. The costs are the 
same but the performance is different. There is a tradeoff – if you want 
the ability to change out the socks you go with the CXR model but the 
performance of the unit is different compared to the CX model. The 
Static Holding Time for the CX100 is 22 days for the CXR100 is 16 days. 
The CXR has a removable sleeve in the holding cavity that keeps the 
socks in place. That removable sleeve is made of a hardened plastic. 
This sleeve introduces more direct heat into the cavity of the unit thus 
having a shorter Static Holding Time.


2. What is Static Holding Time? Static Holding Time is a value we use to 
judge the performance of a unit. The value is made up of the amount of 
LN2 in liters divided by the NER performance. This will give you the 
number of days or length of time a unit can hold product until it 

Re: [ccp4bb] Fwd: dry Shipper made in China

[Artem Evdokimov]

Dry shippers are often featured on auction sites for used equipment and
sometimes can be found for huge discounts...

Artem

- Cosmic Cats approve of this message


On Fri, Jan 25, 2019 at 8:36 AM Muhammad Imran  wrote:

> Dear Community members,
>
> We wanted to buy molecular dimension dry shipper CX100 and universal puck
> starter kit. However due to increase in dollar price compared to Pakistani
> rupee, our budget does not allow to buy these items.
> We tried to search an alternate and found one from Biobase China (details
> attached). I want to know if any one have used it or have experience that
> it can also hold UNIPUCK and be accepted at light sources (Diamond, ESRF,
> SESAME etc).
> Thanks if you can spare time for this.
>
> --
>
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[ccp4bb] Fwd: 2 EMDB Job Opportunities at EMBL-EBI

[David Armstrong]

Please see the following job opportunities available with our colleagues 
at EMDB.



Kind Regards,

David Armstrong



 Forwarded Message 
Subject:2 EMDB Job Opportunities at EMBL-EBI
Date:   Tue, 22 Jan 2019 10:46:19 +
From:   Osman Salih 
To: 'David Armstrong' 



Hi Dave,

Could you please circulate the following message to the CCP4 mailing list?

Thanks and best wishes,

Oz


--

Dear CCP4,

There are two fantastic opportunities to be part of the exciting EMDB
Team at EMBL-EBI in Hinxton near Cambridge. EMBL-EBI is a world-leader
in archiving and disseminating 3D biomacromolecular and cellular
structure data and plays a key role in the dissemination of 3D electron
microscopy (EM) data through the EMDB (emdb-empiar.org) and EMPIAR
(empiar.org) public archives. Specifically, we are looking for:

1. A Scientific Programmer
(https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01331)
2. A Data Scientist
(https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01332)

The closing dates for both positions are 6th February 2019.

Good luck!

EMDB
EMBL-EBI, Wellcome Genome Campus,
Hinxton, Cambridgeshire,
CB10 1SD. UK




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[ccp4bb] Fwd: Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Dirk Kostrewa]

Sorry for spamming the CCP4BB with this e-mail meant for Kay, only - I 
accidentally used the "Reply All" button instead of the "Reply" button 
... ;-)


Anyway, I wish the CCP4 community a Happy New Year!

Cheers,

Dirk.

 Forwarded Message 
Subject: 	Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu 
workstation

Date:   Mon, 7 Jan 2019 14:12:05 +0100
From:   Dirk Kostrewa 
Reply-To:   dirk.kostr...@lmu.de
To: CCP4BB@JISCMAIL.AC.UK



Lieber Kay,

ich wünsche Dir ein Frohes und Gesundes Neues Jahr!

Ich staune auch, dass es anscheinend keine "3D-Ready"-Monitore mehr 
gibt! Wir haben einmal versuchsweise einen 144 Hz ASUS Monitor ohne 
"3D-Ready" gekauft - leider hat da die Synchronisation mit der 
Stereo-Brille nicht funktioniert ...


Mit unseren alten 3D-Ready-Monitoren haben wir unter Scientific Linux 
7.6 bisher keine 3D Stereo-Probleme beobachten können. Die 
Nvidia-Treiber kommen aus dem ELRepo-Repository. Habt Ihr die 
Stereo-Probleme noch?


Liebe Grüße,

Dirk.

On 20.12.18 22:28, Kay Diederichs wrote:
Unfortunately, monitors with built-in emitter are no longer being 
manufactured. The NVIDIA website has not been updated for years. So 
that path leads nowhere.


Stereo has worked well for us (for existing monitors with built-in 
emitter, and with Quadro cards /USB emitter) until and including 
CentOS 7.5. Recently, this stopped after updating to CentOS 7.6 - coot 
finds the stereo-capable hardware and reports the switch to stereo, 
but the monitor does not flip the pictures. We are investigating. We 
are using the Nvidia drivers through the EPEL repository.


best,

Kay


On Thu, 20 Dec 2018 16:11:56 -0500, David Schuller 
 wrote:



I can see two possible paths here:

1) Make the card work with an emitter

or 2) Switch to a monitor with a built-in emitter

Datasheet on the graphics card:


"3D Stereo support with Stereo Connector1
...
1 VGA/DVI/HDMI/stereo support via adapter/connector/bracket"

The task then is to identify the correct bracket to work with this card,
and find a source for purchase.
Something like this:

https://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_Stereo_Bracket_for_Quadro.html
"PNY Technoligies Stereo Bracket for Quadro FX 3800"

Is this part also compatible with the Quadro P4000? I do not know.

http://www8.hp.com/h20195/v2/GetPDF.aspx/c04658472.pdf
"NVidia 3D Stereo Bracket...
Supports NVIDIA Quadro® K4000, K5000, K6000, K4200, K5200,
M4000, M5000, M6000, P4000, P5000, P6000 graphics cards"


Seems promising.

-
Here is a web page listing compatible monitors. You can filter for those
with "built-in emitter"

https://www.nvidia.com/object/3d-vision-displays.html





On 12/20/18 3:45 PM, Adarsh Kumar wrote:

Hello everyone

We have just purchased a Dell workstation for crystallography data 
analysis. We were trying to use Nvidia 3D vision 2 glasses with it, 
but failed to do so. Please help me out with this one. Some relevant 
informationis as follows:

OS: Ubuntu 16.04 LTS
Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
Monitor: Asus VG248QE

Thanks and regards
Adarsh Kumar
Suo Lab
Florida State University College of Medicine



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--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu




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--

**
Dr. Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
WWW:www.genzentrum.lmu.de
strubio.userweb.mwn.de
**



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[ccp4bb] Fwd: Re: [ccp4bb] phase behavior (slightly off-topic)

[Aleksandar Bijelic]

Dear Eugene,

the additive is a metal-polyanion with a net charge of 6- ... yes, NaCl 
affects largely the solubility of the anions, however, the LLPS appears 
within a rather large protein concentration range (10-50 mg/ml = 0.7 - 
3.5 mM) in the presence of e.g. 0.1, 0.5, 1.0, 2.5 and 5.0 mM additive 
but only at NaCl conc = 0.25 M. I will set up conditions with higher 
additive conc to check if the LLPS-region changes with the amount of 
additive.


Am 09.12.2018 um 14:23 schrieb Eugene Osipov:

Hi, Alex,
you did not mention exactly what kind of addictive you use. I suggest 
that amorphous precipitation is due to this addictive as proteins more 
likely to precipitate in presence of polyvalent ions.
May I suggest that sodium chloride could affect solubility of you 
anions and thus zone with higher protein solubility-lower addictive 
contentration are responsible for observed LLPS


сб, 8 дек. 2018 г. в 14:52, Aleksandar Bijelic 
>:


Dear CCP4 Community,

First of all, I want to aplogize in advance for this more or less
off-topic request. I am currently investigating the phase behavior of
Lysozyme (HEWL) in the presence of NaCl and an anionic metal cluster
(additive) using the microbatch under oil technique. Before the
experiment I expected that the additive will might lead to a shift of
the phase boundaries in comaprison to the HEWL-NaCl system, or
maybe to
an increase of the phase space, where nucleation or even crystals
occur.
Unfortunately, the HEWL-NaCl-cluster-system did not exhibit a
textbook-example of a phase diagram as at almost every condition
(different protein, salt and cluster conc.) an amorphous
precipitation
was immediately formed, which in most of the cases became crystalline
within 1-5 days (mostly shower of needles, spherulites and sea
urchins
and sometimes crystals). The transformation from amorphous to
crystalline precipitate was accompanied by liquid-liquid-phase
separation (LLPS), i.e. the amorphous precipitates dissovled
within 1-2
days and LLPS was observed before the crystalline precipitate was
formed. The odd thing is that LLPS was always observed at the same
NaCl
concentration (0.25-0.35 M, but mostly 0.25 M) independent of the
protein or cluster concentration. At the beginning I thought that
I was
located at the edge of a very narrow LLPS-region, however, testing at
higher protein conc. did not change or shift the LLPS conditions
as in
the range of 10-50 mg/ml HEWL (0-50 mg/ml was investigated) and
independet of the cluster conc. (0.1 - 5.0 mM), the LLPS occured
always
at 0.25-0.35 M NaCl. As I am far away from being an expert in protein
phase behavior, I cannot explain this "magical" salt conc. that
induces
at every tested protein and cluster conc. LLPS. Thus, I hope that
somebody of you might have observed the same or a similar behavior
and
is able to explain this to me. Thanks in advance!

Regards,

Aleks



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--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
Research Center of Biotechnology


--
---

Dr. Aleksandar Bijelic

Institut für Biophysikalische Chemie
Universität Wien
Althanstrasse 14
A-1090 Wien

Tel: +43 1 4277 52533
e-Mail:aleksandar.bije...@univie.ac.at






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[ccp4bb] Fwd: [ccp4bb] VERY old mtz file..

[Carter, Charlie]

Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] VERY old mtz file..
Date: November 14, 2018 at 10:16:23 AM EST
To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>>

I’ve found this thread to be most interesting and out of near pathological 
curiosity, I’ve read much of it.

Eleanor’s cameo description in this message makes me curious to know how the 
transition from vax’s and this file in particular, managed to transcend the 
continuity ccp4 strives for. Were MRC files really a significant variant in the 
implementation of mtz binary format to replace labeled column format?

Many thanks, and best to all,

Charlie

On Nov 14, 2018, at 10:04 AM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

You are  all extremely informed and clever!!
This file is part of an old archive of haemoglobin structures from the 1990s.
I suspect they are all generated on a VAX from lcf files when I was "updating" 
the archive..

So now if I have the character I can update them all again, in the unlikely 
event that someone will want to use them!


Thank you all very much
Eleanor

On Wed, 14 Nov 2018 at 14:41, Zhijie Li 
mailto:zhijie...@utoronto.ca>> wrote:
Hi Nick,

I think I've found the machine stamps in the ccp4 lib (Ian Tickle directed me 
to the C programs folder yesterday. Thanks Ian):

ccp4_ssydep.h

#define DFNTI_MBO   1   /**< Motorola byte order 2's compl */
#define DFNTI_IBO   4   /**< Intel byte order 2's compl */

#define DFNTF_BEIEEE1   /**< big endian IEEE (canonical) */
#define DFNTF_VAX   2   /**< Vax format */
#define DFNTF_CONVEXNATIVE 5/**< Convex native floats */
#define DFNTF_LEIEEE4   /**< little-endian IEEE format */



Checking the numbers are quite feasible for MTZ files (not maps because we can 
put anything into MRC/ccp4 map). Yes, the idea is to try all possibilities 
until we can recover miller indices that look normal.

Zhijie


From: Nicholas Devenish mailto:ndeven...@gmail.com>>
Sent: Wednesday, November 14, 2018 9:29 AM
To: Zhijie Li
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] VERY old mtz file..

Hi Zhijie,

Thanks for the answer. I'd read http://www.ccp4.ac.uk/html/mtzformat.html "The 
first 4 half-bytes represent the real, complex, integer and character formats, 
and the last two bytes are currently unused" - and assumed that a) formats 
meant size, given that it was (4,4,4,1) in files I'd seen, though perhaps 
parsers don't really seem to use this. and that b) while this doesn't specify 
endian-ness, one could infer it from whether the two unused zero-bytes came in 
the little-or-big end of the integer. Otherwise there really isn't an encoded 
way to tell if the file was written little or big other than guessing and 
checking if the numbers are sensible?
CCP4 Program Suite: mtz format
www.ccp4.ac.uk
Column types. All columns in an MTZ file are assigned a type, taken from the 
following list. The LABIN line of a particular job connects columns in an input 
MTZ file with the columns expected by the program.




Perhaps this is a (small) flaw in the spec, though nowadays almost everyone 
seems to have moved to little-endian.

Nick

On Wed, Nov 14, 2018 at 2:13 PM Zhijie Li 
mailto:zhijie...@utoronto.ca>> wrote:
>
> Hi Nick,
>
>
> I guessed the machine stamp from MRC/CCP4 format description - half byte 01 
> means BE, half byte 04 means LE. Are these only applicable to intel machines? 
> How are other machine architectures indicated? I do not know. We probably can 
> find the authoritative answer from the CCP4 library, just need a little bit 
> more time...
>
>
> The machine stamp itself should not be affected by the machine's 
> architecture, because it needs to be read before the program knows what the 
> architecture is. Therefore it should be a string instead of a number. In the 
> MRC/CCP4 map specification, it says that only the first two bytes are used.  
> I had seen some home-brew programs taking shortcuts by using the int value of 
> the machine stamp word, and I thought that was smart. Now I realise that this 
> practice has the risk of failing on non-intel machines. So, if it is meant to 
> be half-bytes, interpret it as half bytes!
>
>
> Zhijie
>
>
>
> 
> From: Nicholas Devenish mailto:ndeven...@gmail.com>>
> Sent: Wednesday, November 14, 2018 8:54 AM
> To: Zhijie Li
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] VERY old mtz file..
>
> Hi Zhijie,
>
> Looks like we both had the same thoughts!
>
> On Wed, Nov 14, 2018 at 1:19 PM Zhijie Li 
> mailto:zhijie...@utoronto.ca>> wrote:
>
> The semiBE.mtz has the big endian stamp (0x11 11 00 00 at bytes 9-12 ) 
> put in the header of the original file; 

[ccp4bb] Fwd: Re: [ccp4bb] coiled-coil "degree"

[Jorge Iulek]

My /acknowledgements/ to all that have replied to my question.
So many interesting inputs and points to software; I will be checking in 
the next days.

I will comment upon just some of the observations.

As far as we can, we try to take as "asymmetric unit content" what is 
"expected" (or sometimes, with experimental corroboration) to be the 
functional oligomer, but of course, generally, the most probable one.


We had previously used pisa, but to compare domain-domain contacts. Now 
we will take it again in a helix-helix context. But, together with the 
other software indicated.


Yours,

Jorge


On Tue, Aug 28, 2018 at 6:03 AM, Jorge Iulek > wrote:


   Dear all,


    I am working currently on a structure that, nicely, presents
   two different orientations between its domains when one compares
   monomers of the tetramer in the asymmetric unit.

    I notice, in this nature gift, that a helix, probably central
   (in its role) for the relation (orientation) between the two
   domains,  assumes different relation to other one (helix, that
   belongs to one of the domains) such that they are (significantly)
   more or less "coiled-coiled"one to another, once the domains are in
   the "close" or "open" conformation. We have already analyzed the
   hydrogen bonds and salt bridges that are disrupted (or formed) due
   to the different (domain and helix) conformations.

    I wonder whether there is a metric (easy to evaluate) to
   characterize how much the two helix are "around each other" (id est,
   how much "coiled-coiled" they are) and, preferably, a software to
   calculate this metric.

    Thank you,


   Jorge

   State University of Ponta Grossa

   

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[ccp4bb] Fwd: [ccp4bb] Sulphate or phosphate? (Armin's figures)

[Charles Ballard - UKRI STFC]

Begin forwarded message:

[cid:image001.png@01D42A41.AE0B8B60]




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Re: [ccp4bb] Fwd: Re: [ccp4bb] suggestion of crystallization optimization

[zaigham mahmood khan]

hey Liu

... you got all wonderful suggestion, and they may be time consuming.
Meantime, you may work on the crystals in hand, and follow the suggestions
as mentioned above.

>From my experience, i can tell you that crystal age is also an important
parameter. I will shoot it as soon as i see it in its (semi)-final size.
Leaving crystals in PEG-based solution may not be advantageous. Again, that
was my experience. Also, I noticed PEG skin at the top of the drop, and
several of the crystals were actually got wrapped in the skin while
fishing. Such crystals gave the poorest diffraction. So thats one thing you
may look at it.. (in addition to others, as mentioned above)

Best wishes

-Z


Zaigham Khan, PhD

Icahn School of Medicine at Mount Sinai
Department of Oncological Sciences
1470 Madison Avenue
New York

On Tue, Jun 5, 2018 at 9:39 PM, khevener  wrote:

>
> Good suggestions here.  In situ proteolysis is a new one on me...
>
>
> Sent from my Verizon, Samsung Galaxy smartphone
>
>  Original message 
> From: Artem Evdokimov 
> Date: 6/5/18 1:24 PM (GMT-06:00)
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] suggestion of crystallization optimization
>
> Janet, Patrick, and others beat me to it :)
>
> We have tremendous luck with MMS in cases like this.
>
> I would also suggest looking at 'atypical' additives - the word atypical
> is really not a good choice since the world of additives is pretty much
> infinite, but folks too often tend to take the lazy way out and use the few
> pre-compiled libraries of 'typical additives' that are available
> commercially.
>
> Not to mention that in cases like this a lot of improvement can be
> achieved by exploring protein concentration as a factor (not the same as
> drop ratio, that's also a lazy way out but it's not the same) and by
> switching buffers and salts to other buffers and salts (at the same pH
> even!).
>
> Crystals, protein crystals, with 8A diffraction - you're 65% done. The
> last 35% can take a year :)
>
>
> Artem
>
> - Cosmic Cats approve of this message
>
> On Tue, Jun 5, 2018 at 12:58 PM, Patrick Shaw Stewart <
> patr...@douglas.co.uk> wrote:
>
>>
>> Hi Liuqing Chen
>>
>> You have a lot of good suggestions, but everyone except for Janet has
>> missed out the most important suggestion, and Janet has called it something
>> funny - cross seeding often refers to something else.
>>
>> You may well have a nucleation problem - that's to say many of your
>> screening experiments may be in the metastable zone of your protein's phase
>> diagram.
>>
>> Try making a seedstock with your existing crystals and adding it to *random
>> *screens.  This can be combined with Janet's suggestions 2 (second
>> part), 3, 4, 5, 7, 6 again, and 8.
>>
>> For more information google MMS crystallization, or rMMS crystallization.
>>
>> I hope it works - it very often does!
>>
>> Good luck,
>>
>> Patrick
>>
>>
>>
>>
>>
>> On 4 June 2018 at 21:41, Janet Newman  wrote:
>>
>>> Liuqing Chen,
>>>
>>> Everything that has been said seems reasonable, but there are always
>>> infinite possibilities in crystallisation, so it is more a question of
>>> priorities. Do the easy (or quick) things first. If you have buckets of
>>> prepared protein then what you will try first might be different than if
>>> you have to go and make your protein from scratch each time you set up
>>> crystal trays.
>>>
>>> 1. If you have crystals from an additive screen or seeding - try putting
>>> them in the beam. If you have access to in-plate screening, you can test
>>> the crystals without disturbing them, which will give the best idea of
>>> their native diffraction. Perhaps one of the ugly crystals diffracts well
>>> enough?
>>>
>>> 2. Try cross seeding - seed one or more initial screen(s) (rather than
>>> an optimisation).  Try initial screening with seeding at different
>>> temperatures. If you are currently using vapour diffusion, try microbatch.
>>> Or vice versa.
>>>
>>> 3. Try in-situ proteolysis. Add a very small amount of protease to your
>>> protein sample (chymotrypsin is traditional) - say 1:10,000 or 1:1000
>>> compared to your protein concentration then set up that mixture in initial
>>> screens.
>>>
>>> 4. Is there a ligand/inhibitor/other small molecule that binds? Add that
>>> to your protein before crystallisation. Maybe even try this first!
>>>
>>> 5. Lysine methylation/cysteine modification/other side chain
>>> modifications.
>>>
>>> 6. Try using DSF or some other technique to look at your protein's
>>> stability in the formulation it is in. Maybe you can make happier protein
>>> by changing the pH, buffer or salt.
>>>
>>> 7. If you want to be a little more rigorous, take your protein, and a
>>> number of different proteases, and do a time-course experiment with each
>>> protease (add 1:1000 protease to your protein, then take samples at
>>> timepoints - say 0.5 hours, 1 hour, 5 hours and overnight) then run out on
>>> a gel (or analyse by MS) and see if you come down to a 

[ccp4bb] Fwd: Senior Laboratory Technician - Protein Purification - in the Medicines Discovery Institute at Cardiff University.

[benjamin bax]

We are advertising for a Senior Laboratory Technician Protein Purification in 
the Medicines Discovery Institute at Cardiff University, UK.
 
The goal of the newly-established Medicines Discovery Institute in Cardiff is 
to translate world-leading research on scientific understanding of disease 
mechanisms into innovative therapeutic approaches.  Our vision is to play a 
leading role in discovering new medicines in areas of high unmet need, with a 
particular emphasis on, but not exclusive to, neuroscience and mental health.
 
Closing date: Sunday, 15 July 2018.
 
Interested candidates please apply via University of Cardiff job page:
https://krb-sjobs.brassring.com/TGnewUI/Search/home/HomeWithPreLoad?PageType=JobDetails=30011=5460=7452BR#jobDetails=1239864_5460
 

  
Informal inquiries to:  b...@cardiff.ac.uk  

 





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[ccp4bb] Fwd: Re: [ccp4bb] suggestion of crystallization optimization

[khevener]

Good suggestions here.  In situ proteolysis is a new one on me...

Sent from my Verizon, Samsung Galaxy smartphone
 Original message From: Artem Evdokimov 
 Date: 6/5/18  1:24 PM  (GMT-06:00) To: 
CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] suggestion of crystallization 
optimization 
Janet, Patrick, and others beat me to it :)

We have tremendous luck with MMS in cases like this.
I would also suggest looking at 'atypical' additives - the word atypical is 
really not a good choice since the world of additives is pretty much infinite, 
but folks too often tend to take the lazy way out and use the few pre-compiled 
libraries of 'typical additives' that are available commercially. 
Not to mention that in cases like this a lot of improvement can be achieved by 
exploring protein concentration as a factor (not the same as drop ratio, that's 
also a lazy way out but it's not the same) and by switching buffers and salts 
to other buffers and salts (at the same pH even!). 
Crystals, protein crystals, with 8A diffraction - you're 65% done. The last 35% 
can take a year :)

Artem
- Cosmic Cats approve of this message

On Tue, Jun 5, 2018 at 12:58 PM, Patrick Shaw Stewart  
wrote:

Hi Liuqing Chen
You have a lot of good suggestions, but everyone except for Janet has missed 
out the most important suggestion, and Janet has called it something funny - 
cross seeding often refers to something else.
You may well have a nucleation problem - that's to say many of your screening 
experiments may be in the metastable zone of your protein's phase diagram.
Try making a seedstock with your existing crystals and adding it to random 
screens.  This can be combined with Janet's suggestions 2 (second part), 3, 4, 
5, 7, 6 again, and 8.
For more information google MMS crystallization, or rMMS crystallization.
I hope it works - it very often does!
Good luck,
Patrick




On 4 June 2018 at 21:41, Janet Newman  wrote:
Liuqing Chen,



Everything that has been said seems reasonable, but there are always infinite 
possibilities in crystallisation, so it is more a question of priorities. Do 
the easy (or quick) things first. If you have buckets of prepared protein then 
what you will try first might be different than if you have to go and make your 
protein from scratch each time you set up crystal trays.



1. If you have crystals from an additive screen or seeding - try putting them 
in the beam. If you have access to in-plate screening, you can test the 
crystals without disturbing them, which will give the best idea of their native 
diffraction. Perhaps one of the ugly crystals diffracts well enough?



2. Try cross seeding - seed one or more initial screen(s) (rather than an 
optimisation).  Try initial screening with seeding at different temperatures. 
If you are currently using vapour diffusion, try microbatch. Or vice versa.



3. Try in-situ proteolysis. Add a very small amount of protease to your protein 
sample (chymotrypsin is traditional) - say 1:10,000 or 1:1000 compared to your 
protein concentration then set up that mixture in initial screens. 



4. Is there a ligand/inhibitor/other small molecule that binds? Add that to 
your protein before crystallisation. Maybe even try this first!



5. Lysine methylation/cysteine modification/other side chain modifications.



6. Try using DSF or some other technique to look at your protein's stability in 
the formulation it is in. Maybe you can make happier protein by changing the 
pH, buffer or salt.



7. If you want to be a little more rigorous, take your protein, and a number of 
different proteases, and do a time-course experiment with each protease (add 
1:1000 protease to your protein, then take samples at timepoints - say 0.5 
hours, 1 hour, 5 hours and overnight) then run out on a gel (or analyse by MS) 
and see if you come down to a stable fragment. If you do - then use that 
protease, and while you are waiting for the crystallisation trials to do their 
thing, find out what the end points of the proteolysis fragment are, and make 
that construct.



6. Try a different expression system (different tag, different position of the 
tag, cleave/don't cleave the tag). If the protein is produced in a eukaryotic 
system (and is glycosylated) try a different one to get different glycosylation 
pattern. Try kifunensine treated cells if you are in a mammalian expression 
system.



8. Try the same protein from other species



Janet Newman

Principal Scientist / Director, Collaborative Crystallisation Centre (C3)

CSIRO Material Science and Engineering

343 Royal Parade

Parkville.  VIC. 3052

Australia

Tel +613 9662 7326

Email janet.new...@csiro.au





From: CCP4 bulletin board  on behalf of Liuqing Chen 
<519198...@163.com>

Sent: 04 June 2018 20:57

To: CCP4BB@JISCMAIL.AC.UK

Subject: [ccp4bb] suggestion of crystallization optimization



Hello everyone!



I get a crystal several months ago, but the crystals diffraction 

[ccp4bb] Fwd: [ccp4bb] suggestions on a microscope for Crystallography

[Daniel M. Himmel, Ph. D.]

-- Forwarded message --
From: Daniel M. Himmel, Ph. D. 
Date: Wed, Mar 7, 2018 at 12:23 AM
Subject: Re: [ccp4bb] suggestions on a microscope for Crystallography
To: Chandramohan Kattamuri 


My best experience was with Leica microscopes, such as the S6E.
Leica microscopes have optics that are at least as good as
Zeiss, Olympus, and Nikon, with a larger working distance
between the specimen stage and the objective lens.  That made
it much easier to manipulate, harvest, and flash cool crystals.  For all
the accessories that Leica supplies (light source, camera mount,
etc.), you'll have to check the web site and speak with a Leica
rep. to customize the microscope for your purposes.  -Daniel


On Tue, Mar 6, 2018 at 9:06 PM, Chandramohan Kattamuri <
1c5b7cb6c764-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi
>
> I'm looking for suggestions on a good microscope for looking at crystals,
> which includes polarization, light source (fiber optics), crosshairs and
> camera mount.  What Models and make?
>
> Thanks in advance
>
> Chandra
>
>
>
>
>

[ccp4bb] Fwd: Fwd: Beamline Scientist position available at the EMBL-Grenoble for the ID23-2 and/or ID29 MX beamlines at the ESRF

[andrewmc]

Dear all,

We have an opening for a highly motivated scientist in the Synchrotron 
Crystallography team at the EMBL Grenoble Outstation.
This team works in close collaboration with the ESRF Structural Biology 
Group in the operation and development of high performance
structural biology beamlines with the aim of impacting on challenging 
structural biological problems. Towards this goal, as well as
providing world leading experimental facilities, the EMBL-ESRF Joint 
Structural Biology Group also develops advanced instrumentation

and data collection methods.

The successful candidate will contribute to the operation and 
development of methods for biological micro-crystallography on the ESRF
beamlines ID23-2 and/or ID29. The recent upgrade of ID23-2 to a high 
intensity microfocus beam (~2 um in diameter), and installation
of a high performance MD3-Up diffracometer represents an excellent 
opportunity to further develop techniques in biological micro-
crystallography. This position also allows the opportunity to contribute 
in the complete upgrade of ID29 to provide an extremely high
intensity, tunable, and microfocus beamline for serial crystallography 
data collection. He/She is expected to actively participate in local
and international initiatives aimed at the further development of 
synchrotron serial and micro-crystallography techniques required to 
maximise the scientific potential of ID23-2 and ID29 post ESRF Extremely 
Brilliant Source upgrade.


The successful candidate should have a PhD degree in Structural Biology 
or a related discipline and a minimum three years of post-doctoral 
experience in MX data collection and analyses. A practical knowledge, or 
an interest, in synchrotron beamline
instrumentation and developing new methods for micro-crystallography at 
advanced light sources is essential. The candidate
should be familiar with the latest MX software developments. Experience 
in computer programming would be advantageous.


The closing date for applications is the 31st of March and interviews 
are currently planned for the 15th of May.


For more information please see:
https://www.embl.fr/jobs/searchjobs/index.php?ref=GR_00116

Best regards,

Andrew

--
Andrew McCarthy
EMBL Grenoble Outstation
71, avenue des Martyrs
CS 90181
38042 Grenoble Cedex 9
France

Tel: +33 4 76 20 7276

[ccp4bb] Fwd: Crystallography job opportunities at HarkerBio in Buffalo, NY

[Eric Larson]

Hello community.

HarkerBIO is structural biology-focused biotechnology company based in
Buffalo, NY with a close relationship to the renowned Hauptman-Woodward
Medical Research Institute.  We are rapidly growing and are seeking to
quickly fill a few open crystallography/structural biology positions.
Please see the the job description below and submit your resume/CV along
with a cover letter to care...@harkerbio.com.

thank you.
Eric


*Scientist/Senior Scientist/Lead/Director: Structural Biology*


*Summary*

An opportunity to participate in (or, if sufficiently qualified, lead) our
structural biology team work. Bring your considerable experience in
structure determination and analysis towards advancing client-focused and
internal drug discovery and technology development efforts.



*Responsibilities & Duties*

1.   Lead from the lab: generate structures (protein, protein
complexes, etc.) with hands-on involvement throughout the entire process
from gene to structure and beyond.

2.   Collaborate, coordinate and enable: construct design,
expression/purification trials, biochemistry and biophysics – collaboration
in tightly matrixed environment is a must.

3.   Communicate: work in an integrated team together with project
leads, senior staff, and Clients. Write detailed reports, lead
teleconference and in-person meetings with Clients. Lead technical meetings
and team meetings as appropriate with level.

4.   Innovate: proactively work on improvements of existing
technologies, discovery of new tools and technologies, contribute to the
internal Discovery projects.

5.   Grow & Train: advance your knowledge and repertoire of techniques.
Learn orthogonal techniques from your Colleagues. Mentor and train others
in the art and science of Structural Biology.


*Essential Qualifications and Background*

1.   Ph.D. in Structural Biology, Biochemistry, or other appropriate
field.

2.   Expert in preparation and crystallization of proteins, protein
assemblies, protein-small molecule complexes, etc. Membrane protein
experience is a plus.

3.   Mastery of effective data collection at modern synchrotron
facilities.

4.   Mastery of structure determination techniques and software.

5.   Multi-tasking and efficient time/effort management.

6.   Excellent interpersonal and communication skills.

7.   Ideal candidate has 5+ years of hands-on gene-to-structure
experience in a pharma/biotech setting. Other experience levels will be
considered – level of responsibility will be scaled accordingly.



*Additional Qualifications for Leadership level*

1.   Strong leadership experience in matrixed team environment (2+
years leading a team in Pharma or Biotech).

2.   Demonstrated capacity to build, motivate, and manage a team of
exceptional Structural Biologists.

3.   Proven ability to apply orthogonal techniques and knowledge
towards solving Discovery challenges (having SPR, NMR, MS, cryoEM,
Enzymology experience is highly advantageous).

4.   Experience initiating and managing multiple external
collaborations.

5.   The ability to represent one’s company in discussions with Clients
& Partners, good situational and business awareness, high level of
presentation and discussion skills – the ability to present complex ideas
and results in an elegant, concise, and effective manner is a must.

6.   Experience with the budgeting process, practical awareness and
application of basic business accounting and cost control skills.

-- 
_
Eric Larson, PhD
HarkerBIO, L.L.C.
700 Ellicott Street,
Buffalo, NY 14203

eric.lar...@harkerbio.com



-- 
_
Eric Larson, PhD
HarkerBIO, L.L.C.
700 Ellicott Street,
Buffalo, NY 14203

716-898-8658 <(716)%20898-8658>
eric.lar...@harkerbio.com

Re: [ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

[Eugene Osipov]

Hi, Yuvraj,
I can suggest two methods:
1) collect a dataset at room temperature
2)  crystallize your protein in cryoconditions. That is add 25 % of
glycerol to your crystallization conditions and perform small optimization
in terms of precipitant concentration.

2017-12-29 7:55 GMT+03:00 Prem Prakash :

>
> -- Forwarded message --
> From: Prem Prakash 
> Date: Fri, Dec 29, 2017 at 10:22 AM
> Subject: Re: [ccp4bb] how to improve the diffraction quality of the
> crystals and avoid icerings
> To: zaigham mahmood khan 
>
>
> Hi, Yuvraj
> Initially I also faced similar problems, then I tried various combinations
> of different additives in the crystallization drop. Then I got relatively
> good diffraction data (2.8 Angstrm) in 0.01mM Bacl2 (in my case). In my
> protein structure I can see the Ba2+ ion bound to the intersubunit
> junctions which probably results some extent of decreased degree of
> freedom. Of course you also need the optimization of cryoprotectant as well
> as I can see Glycerol is giving you good resolution compare to others.
>
> Good luck
> Prem
>
> On Fri, Dec 29, 2017 at 2:06 AM, zaigham mahmood khan <
> mahmood.zaig...@gmail.com> wrote:
>
>> Yuvraj
>>
>> This is a tough call. may be you need to look at this database:
>>
>> http://web.archive.org/web/20111011202903/http://idb.exst.ja
>> xa.jp/db_data/protein/search-e.php
>>
>> Importantly, when you click on "ex" for the tab, "cryoprotectant", a
>> window will pop up and you can read different kinds of cryoprotectants that
>> have been successfully attempted in the past. Off-course, this also depends
>> on type of precipitant that you used for crystallization. Apparently, this
>> seems as glycerol worked better in your case, may be because you have
>> salt-based precipitant.
>>
>>
>>
>> Best wishes
>>
>> -Z
>>
>>
>> Zaigham Mahmood Khan, PhD
>>
>> Icahn School of Medicine at Mount Sinai
>> Department of Oncological Sciences
>> 1470 Madison Avenue
>> 
>> New York
>> 
>>
>> On Thu, Dec 28, 2017 at 8:28 AM, YUVARAJ I  wrote:
>>
>>> Respected All,
>>>  I have crystallized a protein. It is forming big crystals, I have
>>> checked in the home source,
>>> Without cryoprotectant - No diffraction (blank)
>>> with Ethylene glycol- No diffraction (blank)
>>> with PEG 3350 - 7A diffraction and No ice rings
>>>  with Glycerol - 3.5A diffraction with ice rings
>>>
>>> I have tried soaking with glycerol different concentrations 10-30%
>>> glycerol from 30 secs to 5 min.
>>> No improvement in the diffraction quality.
>>>
>>> How to improve the diffraction quality of the crystals and avoid the big
>>> ice ring.
>>>
>>> I have attached the diffraction image with this mail.
>>>
>>> Thanks in advance for your valuable suggestions
>>>
>>> Regards
>>> Yuvaraj
>>>
>>>
>>> --
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
>


-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com

[ccp4bb] Fwd: [ccp4bb] how to improve the diffraction quality of the crystals and avoid icerings

[Prem Prakash]

-- Forwarded message --
From: Prem Prakash 
Date: Fri, Dec 29, 2017 at 10:22 AM
Subject: Re: [ccp4bb] how to improve the diffraction quality of the
crystals and avoid icerings
To: zaigham mahmood khan 


Hi, Yuvraj
Initially I also faced similar problems, then I tried various combinations
of different additives in the crystallization drop. Then I got relatively
good diffraction data (2.8 Angstrm) in 0.01mM Bacl2 (in my case). In my
protein structure I can see the Ba2+ ion bound to the intersubunit
junctions which probably results some extent of decreased degree of
freedom. Of course you also need the optimization of cryoprotectant as well
as I can see Glycerol is giving you good resolution compare to others.

Good luck
Prem

On Fri, Dec 29, 2017 at 2:06 AM, zaigham mahmood khan <
mahmood.zaig...@gmail.com> wrote:

> Yuvraj
>
> This is a tough call. may be you need to look at this database:
>
> http://web.archive.org/web/20111011202903/http://idb.exst.
> jaxa.jp/db_data/protein/search-e.php
>
> Importantly, when you click on "ex" for the tab, "cryoprotectant", a
> window will pop up and you can read different kinds of cryoprotectants that
> have been successfully attempted in the past. Off-course, this also depends
> on type of precipitant that you used for crystallization. Apparently, this
> seems as glycerol worked better in your case, may be because you have
> salt-based precipitant.
>
>
>
> Best wishes
>
> -Z
>
>
> Zaigham Mahmood Khan, PhD
>
> Icahn School of Medicine at Mount Sinai
> Department of Oncological Sciences
> 1470 Madison Avenue
> 
> New York
> 
>
> On Thu, Dec 28, 2017 at 8:28 AM, YUVARAJ I  wrote:
>
>> Respected All,
>>  I have crystallized a protein. It is forming big crystals, I have
>> checked in the home source,
>> Without cryoprotectant - No diffraction (blank)
>> with Ethylene glycol- No diffraction (blank)
>> with PEG 3350 - 7A diffraction and No ice rings
>>  with Glycerol - 3.5A diffraction with ice rings
>>
>> I have tried soaking with glycerol different concentrations 10-30%
>> glycerol from 30 secs to 5 min.
>> No improvement in the diffraction quality.
>>
>> How to improve the diffraction quality of the crystals and avoid the big
>> ice ring.
>>
>> I have attached the diffraction image with this mail.
>>
>> Thanks in advance for your valuable suggestions
>>
>> Regards
>> Yuvaraj
>>
>>
>> --
>>
>>
>>
>>
>>
>>
>>
>>
>

[ccp4bb] Fwd: X-ray Lab Manger Birbeck University of London- Permanent Post

[Nicholas Keep]

A reminder this vacancy closes on Sunday.

There is a vacancy for an X-Ray Laboratory Manager at the Institute for 
Structural and Molecular Biology at Birkbeck/UCL based at Birkbeck, 
University of London.


see https://tinyurl.com/y7jgfmr5

This is a permanent University Funded post.  A brief description of the 
role is below and informal enquiries can be made to me 
(n.k...@mail.cryst.bbk.ac.uk). Closing date is the end of the 10th 
December 2017.


Best wishes

Nick


The Laboratory Manager role will ensure efficient day-to-day running of 
the X-ray Laboratory (including X-ray generators, detectors and 
crystallisation robots) for research staff and students in Biological 
Sciences, the ISMB and for external collaborators and hirers of the 
equipment; ensure that all safety procedures in the laboratory are 
implemented; provide training in use of equipment and to give general 
assistance in crystallography to students and research staff; keep 
abreast of new technologies and methodologies and assess and advise on 
the purchase of new equipment, software, and reagents.
The role holder will coordinate trips to synchrotrons and organise 
Beamline applications. The role holder will also contribute to teaching 
in the department through design, deliver and supervision of practicals, 
tutorials and projects in the general area of molecular biology and 
crystallography


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Fwd: divulgacao bolsa, obrigada

[Teresa Santos Silva]

Dear all



I'd like to draw your attention to the postdoc position in protein
crystallography, currently open in my group at UCIBIO-NOVA (Faculty of
Science and Technology, NOVA University of Lisbon, Portugal).



I am a young PI interested in protein-ligand interactions for
structural-based drug design and the Postdoc will be integrated into my
research team, currently holding 9 full-time people. The fellowship will be
awarded for a period of 12 months, eventually extended using other funding
schemes.



Candidates should hold a PhD in chemistry, biochemistry or related areas
and experience in structural biology. It is mandatory that the candidate
has proven know-how in protein cloning, expression and purification,
crystallization, data collection, structure determination and model
refinement. Preference will be given to candidates with experience in
different expression systems (bacterial, yeast, insect and mammalian) and
biophysical methods for characterizing protein-ligand interactions. The
candidate should be able to develop work autonomously.



Work Plan: During the time of the fellowship the candidate will be involved
in expression, purification and crystallization of soluble proteins that
are important targets for drug development. Biophysical methods will be
applied to determine protein-ligand interaction and structure determination
will be carried out in the presence of the best hits. Model analysis will
allow rationalize the structural determinants that control ligand binding.



Application deadline is December 5th .

For more information please check the following link:

http://www.eracareers.pt/opportunities/index.aspx?task=global=94638



I am happy to answer all your questions

Kind regards

teresa


Unique identifier: 1c293f55-6fac-403e-b737-b1faf2575b77


*1. Descrição do cargo/posição/bolsa*
*1. Job description*
--
*Job:*
Research Fellowship for a PhD holder

*Job/Fellowship Reference:* PTDC/QEQ-MED/1902/2014

*Main research field:* Chemistry

*Sub research field:* Biochemistry

*Job summary:*

One fellowship for a PhD holder is opened under the scope of the project
“Carbon monoxide guided shuttles (COGSs) to fight Rheumatoid Arthritis” /
NOVA.ID.FCT – Associação para a Inovação e Desenvolvimento da FCT,
(PTDC/QEQ-MED/1902/2014),  which is financed by national funds from
FCT/MCTES (PIDDAC)

*Job description:*

*1. Scientific area: *Structural Biology, Biochemistry, Chemistry



*2*. *Admission Requirements:* The fellowship is dedicated to candidates
holding a PhD in chemistry, biochemistry or related areas and experience in
structural biology. It is mandatory that the candidate has proven knowhow
in protein cloning, expression and purification, crystallization, data
collection, structure determination and model refinement. Preference will
be given to candidates with experience in different expression systems
(bacterial, yeast, insect and mammalian) and biophysical methods for
characterizing protein-ligand interactions. The candidate should be able to
develop work autonomously.



*3. Work Plan*: During the time of the fellowship the candidate will be
involved in expression, purification and crystallization of soluble
proteins that are important targets for drug development. Biophysical
methods will be applied to determine protein-ligand interaction and
structure determination will be carried out in the presence of the best
hits. Model analysis will allow rationalize the structural determinants
that control ligand binding.



   1. *Rules and Regulations::*Law Nr. 40/2004, of 18th August altered and

republish by Decree-Law nº 202/2012 of August 27th (Scientific Research
Fellow Statute) and altered by the Decree-Law nº233/2012 of October 29th
and by the Law nº12/2013 of January 29th. Regulations for Advanced Training
and Qualification of Human Resources, I.P in force (
http://www.fct.pt/apoios/bolsas/docs/RegulamentoBolsasFCT2015.pdf*).*



   1. *Working location* *and superviror:*  The work is to be carried out
   at the Departament of Chemistry, at Faculdade de Ciências e Tecnologia da
   Universidade NOVA de Lisboa (FCT-NOVA) under the scientific supervision of
   Dr. Teresa Santos-Silva.



   1. *Fellowship duration*: The fellowship will last for 12 months,
   scheduled to begin in December 2017. The scholarship contract may be
   renewed during the project.



   1. *Salary and benefits:  *The amount of the fellowship corresponds to €
   1.495, according to the table of values ??of grants awarded directly by
   FCT, I.P. in the country (http: // www.fct.pt/apoios/bolsas/valores),
   and the payment is made monthly by bank transfer.



   1. *Selection methodology*: The candidates will be evaluated according
   to their CV (40%) and proven lab experience (60%). In case of a tie, an
   interview will be requested and the final grade will be defined by the
   average