Re: [ccp4bb] defining chiral center in .cif file for ligand atom linked to amino acid side chain

[Paul Emsley]

On 05/11/2020 20:26, George Lountos wrote:



I wanted to check to see what the proper way to include a chiral 
center definition to the .cif file.


I have a ligand that is covalently attached to a cys side chain and I 
wanted to adjust the chirality of the atom of the ligand attached to 
the Cys sulfur but I only have the .cif file for the ligand molecule 
and not sure how to add the protein Cys residue S atom to the chiral 
center definitions so that REFMAC can properly read the file. Any 
suggestions or directions would be appreciated.




You should first follow the standard protocol to make a link using 
CCP4i2 or Coot. If that doesn't do what you want to do then we can continue.



As a matter of interest, is a chiral centre being introduced by the 
formation of the link (e.g. Michael addition) or is a neighboring atom 
being substituted by the SG? The former is a more tricky case.



Paul.





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[ccp4bb] defining chiral center in .cif file for ligand atom linked to amino acid side chain

[George Lountos]

Hi everyone:

I wanted to check to see what the proper way to include a chiral center 
definition to the .cif file.

I have a ligand that is covalently attached to a cys side chain and I wanted to 
adjust the chirality of the atom of the ligand attached to the Cys sulfur but I 
only have the .cif file for the ligand molecule and not sure how to add the 
protein Cys residue S atom to the chiral center definitions so that REFMAC can 
properly read the file. Any suggestions or directions would be appreciated.

Thanks,
George




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[ccp4bb] CCP4 Online at risk

[Uski, Ville (STFC,RAL,SC)]

Dear ccp4bb,

Just to let you know that the CCP4 Online service 
(https://ccp4online.ccp4.ac.uk) is currently 'at risk'. If you notice that you 
fail to connect to the server, refreshing your browser is usually enough to get 
things working again.

This is due a recent firewall upgrade. It should get back to normal in the next 
days. Apologies for any inconvenience.

Best wishes,

Ville

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[ccp4bb] NIH-funded Postdoc in Membrane Protein Structural Biology, Nebraska, USA

[Alex Vecchio]

Dear ccp4 Community,

I would like to bring your attention to an open NIH-funded Postdoc position
in the Vecchio Lab  at the University of
Nebraska-Lincoln. We are looking for someone with experience in membrane
protein biochemistry and structural biology techniques. For further
information, please read our ad at the Biophysical Society website:
https://biophysics-jobs.careerwebsite.com/job/postdoctoral-fellow-in-membrane-protein-structural-biology/55072971/

To apply or for further information, please contact me via the information
below.

All the best,
*Alex J. Vecchio, Ph.D.*
*Assistant Professor*

University of Nebraska–Lincoln

Department of Biochemistry

Center for Integrated Biomolecular Communication

avecc...@unl.edu

1 [402] 472-2933



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Re: [ccp4bb] how to calculate the volume of a small molecule

[Tan, Kemin]

Dear Vincent and Harry,

Thank you for your information and suggestion!

Kemin

On 11/5/20, 3:44 AM, "CCP4 bulletin board on behalf of Harry Powell - CCP4BB" 
 wrote:

Hi

If it’s just organic, use 18 Å^3 per non-hydrogen - e.g. glucose (C6H12O6) 
occupies around 12*18 ~= 216Å^3. Atoms like S and P add a little more, but for 
mental artihmetic and a quick estimate it doesn’t amount to a hill of beans.

H

> On 5 Nov 2020, at 09:25, vincent Chaptal  wrote:
> 
> Dear Kemin, 
> 
> I use VOIDOO from Upsala. 
> 
> Best
> Vincent
> 
> Le 04/11/2020 à 21:05, Tan, Kemin a écrit :
>> Dear all,
>>  
>> Is there a way to calculate or estimate the volume of a small molecule 
within CCP4 or with other programs?
>>  
>> Thanks,
>>  
>> Kemin 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> 
> -- 
> Vincent Chaptal, PhD
> Director of GdR APPICOM
> Drug Resistance and Membrane Proteins Lab
> 
> MMSB -UMR5086
> 7 passage du Vercors 
> 69007 LYON
> FRANCE
> +33 4 37 65 29 01
> http://www.appicom.cnrs.fr
> http://mmsb.cnrs.fr/en/
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] PhD positions available

[Harmer, Nicholas]

Hi everyone,

I have three PhD opportunities available in my lab for students interested in 
structural biology. If you know anyone who might be interested please pass this 
message on to them!

The Living Systems Institute where I am based has funded positions available in 
our PhD programme 
(https://www.exeter.ac.uk/livingsystems/research/lsiphdprogramme/). These are 
open to anyone to apply. We have a thriving interdisciplinary structural 
biology team in the institute so as well as my group there are several other 
great teams as well.

Two positions in my lab are available through our local doctoral training 
programme. These are focused on structure-function of enzymes involved in 
polysaccharide biosynthesis from a human/animal pathogen. These will use a 
combination of X-ray crystallography, Cryo-EM, and (hopefully) MicroED as 
appropriate, and we hope to give a great interdisciplinary structural biology 
training. Unfortunately due to funder rules these are only open to UK residents.
http://www.exeter.ac.uk/studying/funding/award/?id=3974
http://www.exeter.ac.uk/studying/funding/award/?id=3991

Thanks!

Nicholas Harmer
Prof. Nicholas Harmer
Associate Professor in Biochemistry
University of Exeter
Ext: 5179
www.exeter.ac.uk
Living Systems Institute, Stocker Road, Exeter, EX4 4QD
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[ccp4bb] Webinar introducing the Diamond II project and cool talk on what to expect from biological X-ray Imaging with these new machines!

[Walsh, Martin (DLSLtd,RAL,LSCI)]

Dear All,  very excited to invite you to join this webinar next Tuesday 10th 
November at 14:00 (UK time) which will briefly introduce the upgrade programme 
for Diamond  - ‘Diamond-II’ which will provide a far brighter and coherent 
source providing the biology community with exciting opportunities for imaging 
of biological cells, tissues at the nanoscale – So it’s a pleasure to have 
Alexandra Pacureanu from the ESRF present her recent work which aptly 
illustrates the potential for biological x-ray imaging as these new sources 
come online

Please do join us – more information in the link below from where you can also 
register for the 1 hour webinar

https://www.diamond.ac.uk/Home/Events/2020/Diamond-II-Webinar--Large-volume-biological-3D-X-ray-nanoImaging-.html


Best,

Martin


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[ccp4bb] Academic Structural Biology Postdoc position at Yale

[Anderson, Karen]

Dear CCP4 list manager,
Could you please post that attached pdf file describing a postdoctoral position 
in my lab for individual with structural biology experience?
Thanks so much,
Karen


Karen S. Anderson, Ph.D.
Professor of Pharmacology and Molecular Biophysics & Biochemistry
Co-Director Developmental Therapeutics, Yale Comprehensive Cancer Center

Yale University School of Medicine
333 Cedar Street, SHM B-350B
P.O. Box 208066
New Haven, CT 06520-8066
Phone: 203-785-4526
Fax: 203-785-7670
email: karen.ander...@yale.edu



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Postdoctoral Position Available_Anderson[2].pdf
Description: Postdoctoral Position Available_Anderson[2].pdf

[ccp4bb] open Structural Biologist position at Rheos Medicines

[Eric Larson]

Hello Bulletin Board members.

We are seeking to expand our structural biology group at Rheos Medicines in 
Cambridge, MA.  Please see the details here: 
https://rheosrx.com/careers/job-detail/?job=364979 and feel free to reach out 
to me if you are interested or if you know someone that may be.

thank you and stay safe.

Eric Larson

eric.xt...@gmail.com



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[ccp4bb] academic-industrial postdoctoral position in Seville, Spain

[Alejandro Panjkovich]

Dear Colleagues,

The CABD in collaboration with CITRE, a Bristol-Myers Squibb Company is
offering a postdoctoral position on the groundbreaking topic of targeted
protein degradation, in the context of an academic-industrial research
collaboration. The project involves studying and understanding fundamental
aspects of targeted protein degradation, involving molecular glue and
heterobifunctional degraders (aka PROTACs) of enormous therapeutic
potential. We are looking for a talented scientist with:
-PhD in a relevant discipline, such as structural biology, computational
biology, bioinformatics or related fields, accompanied by original research
publications.
-Experience in understanding protein structures and sequences from a
computational perspective, combined with a strong interest in evolution and
fundamental principles.
-Strong expertise in scripting and programming (e.g. R, Python, C++ or
others), machine/deep learning and methods development experience is a plus.
-Attention to detail and capacity to communicate technical/scientific
concepts clearly and concisely to audiences of varied backgrounds.
-Verbal and written English language fluency.

The position will be shared between the CABD and CITRE in Seville, Spain.
Please send a short motivation letter, CV and 2 contacts for references to
Damien Devos  and Alejandro Panjkovich <
alejandro.panjkov...@bms.com>.

Please feel free to share this information at your institutes and with
interested colleagues.

Best regards,

Sasha

--



Alejandro Panjkovich

Senior Scientist - Predictive Sciences

Office+34 955 001 734

E-mailalejandro.panjkov...@bms.com

Bristol Myers Squibb



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Re: [ccp4bb] how to calculate the volume of a small molecule

[Harry Powell - CCP4BB]

Hi

If it’s just organic, use 18 Å^3 per non-hydrogen - e.g. glucose (C6H12O6) 
occupies around 12*18 ~= 216Å^3. Atoms like S and P add a little more, but for 
mental artihmetic and a quick estimate it doesn’t amount to a hill of beans.

H

> On 5 Nov 2020, at 09:25, vincent Chaptal  wrote:
> 
> Dear Kemin, 
> 
> I use VOIDOO from Upsala. 
> 
> Best
> Vincent
> 
> Le 04/11/2020 à 21:05, Tan, Kemin a écrit :
>> Dear all,
>>  
>> Is there a way to calculate or estimate the volume of a small molecule 
>> within CCP4 or with other programs?
>>  
>> Thanks,
>>  
>> Kemin 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> 
> -- 
> Vincent Chaptal, PhD
> Director of GdR APPICOM
> Drug Resistance and Membrane Proteins Lab
> 
> MMSB -UMR5086
> 7 passage du Vercors 
> 69007 LYON
> FRANCE
> +33 4 37 65 29 01
> http://www.appicom.cnrs.fr
> http://mmsb.cnrs.fr/en/
> 
> 
> 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] how to calculate the volume of a small molecule

[vincent Chaptal]

Dear Kemin,

I use VOIDOO from Upsala.

Best
Vincent

Le 04/11/2020 à 21:05, Tan, Kemin a écrit :


Dear all,

Is there a way to calculate or estimate the volume of a small molecule 
within CCP4 or with other programs?


Thanks,

Kemin




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--

Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab


MMSB -UMR5086

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.appicom.cnrs.fr

http://mmsb.cnrs.fr/en/





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