[ccp4bb] Scientist position available at Monte Rosa Therapeutics

[Jennifer Tsai]

Monte Rosa Therapeutics is seeking a talented and highly motivated
Structural Biologist to join the Biomolecular Sciences group. This is an
exciting opportunity to join a team responsible for biochemical and
biophysical characterization and screening of novel small molecule
degraders. The successful candidate will be responsible for Establish
protocols to characterize target proteins for small molecule/protein
binding. Perform protein crystallography, crystal quality optimization,
data collection, structure determination. In charge of organizing and
maintaining internal protein structure deposit for the projects in support
of Monte Rosa’s pipeline of oncology targets. The candidate should exhibit
excellent communication and collaborative skills for working on
cross-functional multi-disciplinary drug discovery teams.

Detailed information about this position is available at this linkedin site:
 *https://shorturl.at/mwOR8 *

Best regards,
Jennifer Tsai



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[ccp4bb] Postdoctoral Position Available at Rutgers University

[Matthew Neiditch]

An NIH-funded postdoctoral position is available at Rutgers University - New 
Jersey Medical School to study the structure and function of novel bacterial 
cytidine deaminases and their regulatory RNAs. In addition to a Ph.D., the 
ideal candidate will have a strong background in macromolecular X-ray 
crystallography, cryoEM, biochemistry, protein purification, and molecular 
biology. Candidates with demonstrated success in another field and a strong 
commitment to learning X-ray crystallography and cryoEM will also be 
considered. A working knowledge of bacterial genetics is a plus. This project 
is an important component of a long-term collaboration with Dr. Christopher 
Waters (Michigan State University), and the ability to communicate ideas and 
work collaboratively as a member of a highly motivated team is essential.

Please submit your CV to matthew.neidi...@rutgers.edu with the subject line 
Postdoctoral Position Applicant.

Matthew Neiditch
Dept. of Microbiology, Biochemistry, and Molecular Genetics
New Jersey Medical School
Rutgers University



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[ccp4bb] Postdoctoral position in Bethesda, MD, US

[Marzena Pazgier]

A postdoctoral position is available immediately to participate in an
inter-disciplinary research program in structural immunology at the
Uniformed Services University of the Health Sciences (USU) in Bethesda, MD.
Candidates are expected to work on ongoing research projects in structural
biology with the aim to understand the molecular basis of the adaptive
immune response to HIV-1 and Sars-Cov2 and the ultimate goal to develop new
protein-based therapeutics and novel vaccine concepts. Qualifications for
the position include: a strong research interest and experience in
molecular cloning, protein expression, molecular interaction analysis,
X-ray crystallography and/or Cryo-EM and excellent
interpersonal/oral/written communication skills.



Candidates need to be highly motivated individuals who enjoy working as
part of a dynamic, collaborative and multidisciplinary team. Preference
will be given to candidates with exceptionally strong experimental skills,
a strong record of peer-reviewed publications, and a demonstrated
commitment to basic research. Qualified candidates should have a doctorate
in chemistry/biochemistry, microbiology, immunology or a closely-related
field. Candidates at any career stage are invited.



USU is in Bethesda, MD directly across the street from the NIH, and is
therefore part of an extraordinarily vibrant local biomedical research
community. Our research projects take advantage of recently established
Core facilities for Nextgen sequencing, Bioinformatics and Structural
Biology analyses. USU has a strongly collaborative environment, with weekly
Immunology data club and journal club meetings, as well as regular research
seminars featuring local and invited speakers.



Candidates should apply by submitting a CV plus names and contact
information for 3 references directly to marzena.pazg...@usuhs.edu



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[ccp4bb] Job advert for a structural biology/biophysics role in PROTAC drug discovery

[David Zollman (Staff)]

Dear all,



We have a particularly exciting job opportunity in our lab, the PROTAC drug 
discovery collaboration between the group of Prof Alessio Ciulli at the 
University of Dundee and Boehringer Ingelheim. Our group are world leaders in 
the field of PROTACs, which has rapidly become one of the hottest topics in 
drug discovery. We are looking to recruit one new team member to help expand 
our structural biology, protein production and biophysical efforts.

If you have relevant doctoral/post-doctoral experience and are interested in 
joining a highly motivated, dynamic, interdisciplinary group at the interface 
of academia and industry, the deadline for application is Thursday 18th 
February. The post is available for an immediate start, with funding until 31st 
August 2023 in the first instance. Salary will depend on experience, but the 
appointment will be at Grade 7 on the University's salary scale (between 
£32,817 - £40,322). The full job advert including details on how to apply can 
be found at 
https://ig5.i-grasp.com/fe/tpl_uod01.asp?newms=jj=104360=14197



Best wishes,

David Zollman


The University of Dundee is a registered Scottish Charity, No: SC015096



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Re: [ccp4bb] RCrane in Coot 0.8.9.2 for Mac

[Tim Gruene]

Hi Almudena,

in my Coot 0.9.2, the Calculate menu has the entry 'RCrane launch' as
second last subentry. 

Best,
Tim


On Tue, 9 Feb 2021 13:43:25 + Paul Emsley
 wrote:

> On 09/02/2021 13:33, Almudena Ponce Salvatierra wrote:
> > 
> > I have Coot 0.8.9.2 installed on macOS Catalina. I would like to
> > launch RCrane, but I can't find it under "Extensions".
> > 
> > Does anybody know whether there is a way I can make it work on the
> > version of Coot, or should I rather uninstall it and look for
> > another one?  
> 
> Hi Almudena,
> 
> I consulted the release notes, and it says that RCrane was restored
> in 0.8.9.2, so the fact that you can't find it is perplexing. Maybe
> it moved (I don't recall now, it's been a while).
> 
> Maybe you can find it in a more recent version? (although you might
> find that other things have moved).
> 
> Paul.
> 
> 
> 
> 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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> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgphbiJPOVHp3.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] RCrane in Coot 0.8.9.2 for Mac

[Almudena Ponce Salvatierra]

Found it!

It is under the "Calculate" menu!

Thank you Paul for answering!

Best,

A

El mar, 9 feb 2021 a las 14:44, Paul Emsley ()
escribió:

> On 09/02/2021 13:33, Almudena Ponce Salvatierra wrote:
> >
> > I have Coot 0.8.9.2 installed on macOS Catalina. I would like to launch
> RCrane, but I can't find it under
> > "Extensions".
> >
> > Does anybody know whether there is a way I can make it work on the
> version of Coot, or should I rather
> > uninstall it and look for another one?
>
> Hi Almudena,
>
> I consulted the release notes, and it says that RCrane was restored in
> 0.8.9.2, so the fact that you can't
> find it is perplexing. Maybe it moved (I don't recall now, it's been a
> while).
>
> Maybe you can find it in a more recent version? (although you might find
> that other things have moved).
>
> Paul.
>
> 
>
> 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 https://www.jiscmail.ac.uk/policyandsecurity/
>



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Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

[Paul Emsley]

On 09/02/2021 13:33, Eleanor Dodson wrote:

Yes, I agree.. garish? Rob Nichols?? Can you email this to them directly? E



Yeah, I never liked that colour scheme either. Maybe this is a job for 
Super-Gemmi!

Paul.



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Re: [ccp4bb] RCrane in Coot 0.8.9.2 for Mac

[Paul Emsley]

On 09/02/2021 13:33, Almudena Ponce Salvatierra wrote:


I have Coot 0.8.9.2 installed on macOS Catalina. I would like to launch RCrane, but I can't find it under 
"Extensions".


Does anybody know whether there is a way I can make it work on the version of Coot, or should I rather 
uninstall it and look for another one?


Hi Almudena,

I consulted the release notes, and it says that RCrane was restored in 0.8.9.2, so the fact that you can't 
find it is perplexing. Maybe it moved (I don't recall now, it's been a while).


Maybe you can find it in a more recent version? (although you might find that 
other things have moved).

Paul.



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Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

[David Lawson (JIC)]

…and make this the default 

Garib and Rob cc’d…

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk

From: Eleanor Dodson 
Sent: 09 February 2021 13:33
To: David Lawson (JIC) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

Yes, I agree.. garish? Rob Nichols?? Can you email this to them directly? E

On Tue, 9 Feb 2021 at 13:28, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:
Hi Eleanor,

I’m glad it’s not just me then.
I too tried the grepping option, but my recollection was that that didn’t go 
too well either. It doesn’t help that I’m not very comfortable with MMCIF 
format yet…
Also, I forgot to mention, but was just reminded that you can change “Output 
calculated riding hydrogens to file” to “No” in the Output tab of REFMAC, but 
it still writes them to the MMCIF!
Without wishing to start a lengthy email discussion, can’t we just have the 
option to write an MMCIF without hydrogens from REFMAC?

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk

From: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Sent: 09 February 2021 13:15
To: David Lawson (JIC) mailto:david.law...@jic.ac.uk>>
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

I took this up with pdbe but what with lock down and all I am not too sure what 
the decision was ( or whether there was one) maybe you could start a chat to 
the pdbe lot
Our code was d- 1292109592.

It was a mess - tony Wilkinson was depositing the data from the labs, I had 
been doing refinement from home so we didn’t have a proper deposition 
directory. And then they grumbled about hydrogens with zero occupancy. I 
grepped them out of the Mcciff file but it isn’t the best silution
On Tue, 9 Feb 2021 at 12:29, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:
Hi All,

By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens 
during refinement. It then writes out a PDB file without the hydrogens and an 
MMCIF file that retains these hydrogens. In the latter, you end up with mostly 
hydrogens with unit occupancy and a few with zero occupancy. Upon further 
investigation it seems the latter are mostly polar hydrogens, but some sit at 
the end of side-chains that have been truncated (I don’t want restart the 
discussion about whether you should or should not truncate side-chains). As a 
result, if you use the latter for deposition, which is the only option if you 
use the CCP4I2 “New Deposition Task”, you run into trouble. So my question is: 
how can I stop REFMAC from writing the hydrogens to the MMCIF file (I also 
don’t want to restart the discussion about whether you should or should not 
deposit hydrogens)? The alternative is that I revert to using the more tedious 
option of the pdb_extract server since that works with a PDB file.

Thanks in advance,

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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[ccp4bb] RCrane in Coot 0.8.9.2 for Mac

[Almudena Ponce Salvatierra]

Hello everybody,

I have Coot 0.8.9.2 installed on macOS Catalina. I would like to launch
RCrane, but I can't find it under "Extensions".

Does anybody know whether there is a way I can make it work on the version
of Coot, or should I rather uninstall it and look for another one?

Any help will be much appreciated.

Thank you very much.

Cheers,

Almu



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Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

[Eleanor Dodson]

Yes, I agree.. garish? Rob Nichols?? Can you email this to them directly? E

On Tue, 9 Feb 2021 at 13:28, David Lawson (JIC) 
wrote:

> Hi Eleanor,
>
>
>
> I’m glad it’s not just me then.
>
> I too tried the grepping option, but my recollection was that that didn’t
> go too well either. It doesn’t help that I’m not very comfortable with
> MMCIF format yet…
>
> Also, I forgot to mention, but was just reminded that you can change
> “Output calculated riding hydrogens to file” to “No” in the Output tab of
> REFMAC, but it still writes them to the MMCIF!
>
> Without wishing to start a lengthy email discussion, can’t we just have
> the option to write an MMCIF without hydrogens from REFMAC?
>
>
>
> Dave
>
>
>
> ---
>
> Prof. David M. Lawson
>
> Department of Biological Chemistry,
>
> John Innes Centre,
>
> Norwich,
>
> NR4 7UH, UK.
>
> Tel: +44-(0)1603-450725
>
> Web: https://www.jic.ac.uk/people/david-lawson
>
> Email: david.law...@jic.ac.uk
>
>
>
> *From:* Eleanor Dodson 
> *Sent:* 09 February 2021 13:15
> *To:* David Lawson (JIC) 
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Subject:* Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?
>
>
>
> I took this up with pdbe but what with lock down and all I am not too sure
> what the decision was ( or whether there was one) maybe you could start a
> chat to the pdbe lot
>
> Our code was d- 1292109592.
>
>
>
> It was a mess - tony Wilkinson was depositing the data from the labs, I
> had been doing refinement from home so we didn’t have a proper deposition
> directory. And then they grumbled about hydrogens with zero occupancy. I
> grepped them out of the Mcciff file but it isn’t the best silution
>
> On Tue, 9 Feb 2021 at 12:29, David Lawson (JIC) 
> wrote:
>
> Hi All,
>
>
>
> By default, when you run REFMAC5 run through CCP4I2, it uses riding
> hydrogens during refinement. It then writes out a PDB file without the
> hydrogens and an MMCIF file that retains these hydrogens. In the latter,
> you end up with mostly hydrogens with unit occupancy and a few with zero
> occupancy. Upon further investigation it seems the latter are mostly polar
> hydrogens, but some sit at the end of side-chains that have been truncated
> (I don’t want restart the discussion about whether you should or should not
> truncate side-chains). As a result, if you use the latter for deposition,
> which is the only option if you use the CCP4I2 “New Deposition Task”, you
> run into trouble. So my question is: how can I stop REFMAC from writing the
> hydrogens to the MMCIF file (I also don’t want to restart the discussion
> about whether you should or should not deposit hydrogens)? The alternative
> is that I revert to using the more tedious option of the pdb_extract server
> since that works with a PDB file.
>
>
>
> Thanks in advance,
>
>
>
> Dave
>
>
>
> ---
>
> Prof. David M. Lawson
>
> Department of Biological Chemistry,
>
> John Innes Centre,
>
> Norwich,
>
> NR4 7UH, UK.
>
> Tel: +44-(0)1603-450725
>
> Web: https://www.jic.ac.uk/people/david-lawson
>
> Email: david.law...@jic.ac.uk
>
>
>
>
> --
>
> 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] stop REFMAC5 writing hydrogens to MMCIF file?

[David Lawson (JIC)]

Hi Eleanor,

I’m glad it’s not just me then.
I too tried the grepping option, but my recollection was that that didn’t go 
too well either. It doesn’t help that I’m not very comfortable with MMCIF 
format yet…
Also, I forgot to mention, but was just reminded that you can change “Output 
calculated riding hydrogens to file” to “No” in the Output tab of REFMAC, but 
it still writes them to the MMCIF!
Without wishing to start a lengthy email discussion, can’t we just have the 
option to write an MMCIF without hydrogens from REFMAC?

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk

From: Eleanor Dodson 
Sent: 09 February 2021 13:15
To: David Lawson (JIC) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

I took this up with pdbe but what with lock down and all I am not too sure what 
the decision was ( or whether there was one) maybe you could start a chat to 
the pdbe lot
Our code was d- 1292109592.

It was a mess - tony Wilkinson was depositing the data from the labs, I had 
been doing refinement from home so we didn’t have a proper deposition 
directory. And then they grumbled about hydrogens with zero occupancy. I 
grepped them out of the Mcciff file but it isn’t the best silution
On Tue, 9 Feb 2021 at 12:29, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:
Hi All,

By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens 
during refinement. It then writes out a PDB file without the hydrogens and an 
MMCIF file that retains these hydrogens. In the latter, you end up with mostly 
hydrogens with unit occupancy and a few with zero occupancy. Upon further 
investigation it seems the latter are mostly polar hydrogens, but some sit at 
the end of side-chains that have been truncated (I don’t want restart the 
discussion about whether you should or should not truncate side-chains). As a 
result, if you use the latter for deposition, which is the only option if you 
use the CCP4I2 “New Deposition Task”, you run into trouble. So my question is: 
how can I stop REFMAC from writing the hydrogens to the MMCIF file (I also 
don’t want to restart the discussion about whether you should or should not 
deposit hydrogens)? The alternative is that I revert to using the more tedious 
option of the pdb_extract server since that works with a PDB file.

Thanks in advance,

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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] stop REFMAC5 writing hydrogens to MMCIF file?

[Eleanor Dodson]

I took this up with pdbe but what with lock down and all I am not too sure
what the decision was ( or whether there was one) maybe you could start a
chat to the pdbe lot
Our code was d- 1292109592.

It was a mess - tony Wilkinson was depositing the data from the labs, I had
been doing refinement from home so we didn’t have a proper deposition
directory. And then they grumbled about hydrogens with zero occupancy. I
grepped them out of the Mcciff file but it isn’t the best silution
On Tue, 9 Feb 2021 at 12:29, David Lawson (JIC) 
wrote:

> Hi All,
>
>
>
> By default, when you run REFMAC5 run through CCP4I2, it uses riding
> hydrogens during refinement. It then writes out a PDB file without the
> hydrogens and an MMCIF file that retains these hydrogens. In the latter,
> you end up with mostly hydrogens with unit occupancy and a few with zero
> occupancy. Upon further investigation it seems the latter are mostly polar
> hydrogens, but some sit at the end of side-chains that have been truncated
> (I don’t want restart the discussion about whether you should or should not
> truncate side-chains). As a result, if you use the latter for deposition,
> which is the only option if you use the CCP4I2 “New Deposition Task”, you
> run into trouble. So my question is: how can I stop REFMAC from writing the
> hydrogens to the MMCIF file (I also don’t want to restart the discussion
> about whether you should or should not deposit hydrogens)? The alternative
> is that I revert to using the more tedious option of the pdb_extract server
> since that works with a PDB file.
>
>
>
> Thanks in advance,
>
>
>
> Dave
>
>
>
> ---
>
> Prof. David M. Lawson
>
> Department of Biological Chemistry,
>
> John Innes Centre,
>
> Norwich,
>
> NR4 7UH, UK.
>
> Tel: +44-(0)1603-450725
>
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> Email: david.law...@jic.ac.uk
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[ccp4bb] stop REFMAC5 writing hydrogens to MMCIF file?

[David Lawson (JIC)]

Hi All,

By default, when you run REFMAC5 run through CCP4I2, it uses riding hydrogens 
during refinement. It then writes out a PDB file without the hydrogens and an 
MMCIF file that retains these hydrogens. In the latter, you end up with mostly 
hydrogens with unit occupancy and a few with zero occupancy. Upon further 
investigation it seems the latter are mostly polar hydrogens, but some sit at 
the end of side-chains that have been truncated (I don't want restart the 
discussion about whether you should or should not truncate side-chains). As a 
result, if you use the latter for deposition, which is the only option if you 
use the CCP4I2 "New Deposition Task", you run into trouble. So my question is: 
how can I stop REFMAC from writing the hydrogens to the MMCIF file (I also 
don't want to restart the discussion about whether you should or should not 
deposit hydrogens)? The alternative is that I revert to using the more tedious 
option of the pdb_extract server since that works with a PDB file.

Thanks in advance,

Dave

---
Prof. David M. Lawson
Department of Biological Chemistry,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk




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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



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--
*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
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tenure in accordance with the University's Policy and Procedures for
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Salary Scale:   Lecturer: €54,162 - €86,181 p.a. pro rata

Lecturer below the bar: €40,599 - €55,818 p.a. pro
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Further information for applicants and application material is available
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The closing date for receipt of applications is *Monday, 8th March 2021.*

Applications must be completed online before *12 noon, Irish Standard Time*
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*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
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Re: [ccp4bb] Fixing Modified residue

[Paul Emsley]

On 09/02/2021 07:10, Arunabh Athreya wrote:

Hi

I have been facing a similar problem with a backbone thiocarbonylated 
L-serine residue (here's the SMILES: N[C@@H](CO)C(O)=S  )
This residue was not present in the pre-existing library, so I did the 
following:


 1. Used AceDRG to draw the structure of the residue; saved the
restraints and coordinates as XSR.cif and XSR.pdb.
 2. Opened protein pdb and mtz files in coot and centred on the
residue that I had to mutate (*chain A residue 104 SER (the
residues are numbered from 101 to 122) *)
 3. File -> import CIF dictionary -> XSR.cif (generate a molecule
activated).
 4. Edit -> Change Chain IDs -> (Using residue selection 'whole chain'
of XSR.pdb) to "A".
 5. Edit -> merge molecules -> XSR.pdb and protein.pdb to protein.pdb.
XSR got renumbered as 201.
 6. Edit -> renumber residues -> residue 201 -> apply offset by -97.

Once this was done, the bonds were automatically formed at desired places.
The problem came up when I tried to use real space refine zone. The 
residue 104 ejected from its electron density, and even if I do/don't 
do it, refmac crashes afterwards.


I cannot figure out why Refmac crashes when I insert this XSR residue 
but works ok with all other residues.




1: AceDRG doesn't do drawing, perhaps you meant Lidia

2: Your SMILES is non-optimal - you need to include the carboxylate, not 
an implicitly linked carbonyl, i.e. NC(C(=O)O)C(O)=S


3: $ pyrogen -n 'NC(C(=O)O)C(O)=S'

4: $ acedrg -c XSR-pyrogen.cif -p -o XSR-acedrg

5: hand edit XSR-acedrg.cif: replace non-polymer with L-peptide, replace 
all O1 by O


6: In Coot, File -> read CIF dictionary -> XSR-acedrg.cif

7: In Coot, centre on the SER that you wish to modify

8: In Coot, Calculate -> Modelling -> Replace Residue -> XSR

9: Refmac doesn't crash it refuses to proceed with an inconsistency 
between the model and the dictionary.



Paul.





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