[ccp4bb] Standardised presentation of archived X-ray diffraction data quality metrics for PDB entries, consistent with the PDBx/mmCIF dictionary

[Gerard Bricogne]

Dear all,

 It is probably an all-too-frequent observation that

 (1) the *transfer* of X-ray data quality metrics (DQMs for short) from
 Table 1 in an MX structure paper to the PDB archive can be a lossy
 process, and 

 (2) the *presentation* of those DQMs that are actually archived can be
 surprisingly different across the various wwPDB front-ends to the
 PDB provided by the RCSB, PDBe and PDBj .

 We are pleased to offer a Web tool at 

   https://staraniso.globalphasing.org/table1/

that retrieves all available DQMs from the archived mmCIF file associated
with a PDB entry and presents them in a standardised tabular form. The
corresponding documents have been pre-generated for all relevant PDB entries
and are updated automatically on a weekly basis - either if the PDB entry
itself (model mmCIF) or the published PDBx/mmCIF dictionary [1] has changed.

 The simplest mode of use is to enter the PDB identifier of interest
into the box at the top of the landing page, then click on the Go button. A
facility to access the PDB according to any of 14 other attributes is also
provided. The top of the form for each given PDB entry contains hyperlinks
to the RCSB, PDBe and PDBj presentations of its DQMs, so as to facilitate
comparisons.

 Strict and explicit consistency with the PDBx/mmCIF dictionary [1,2]
has been a major goal in this work: throughout each Table, hovering over an
item in the left-hand side column will show its exact name in the PDBx/mmCIF
dictionary, while hovering over an item value in the right-hand side column
will show the associated item definition in that same dictionary.


 We hope that this tool will prove useful, and will welcome enquiries
and any feedback on it that would enable us to improve it.


 With best wishes,

Clemens and the GPhL developers

[1] https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
[2] https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/



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[ccp4bb] FW: Postdoc position in Structural Data Science at NNF-CPR at the University of Copenhagen (Taylor and Rasmussen groups)

[Nicholas M I Taylor]

Dear all,

Just a friendly reminder that the deadline of our postdoc position is coming up 
soon (16 August).

The full advert and link to the application form can be found here: 
https://employment.ku.dk/faculty/?show=154452

Please contact me (nicholas.tay...@cpr.ku.dk) 
or Simon (simon.rasmus...@cpr.ku.dk) directly 
for further enquiries.

Application deadline:  16 August 2021, 23.59pm CET

Best wishes,

Nicholas

From: Nicholas M I Taylor 
Date: Friday, 9 July 2021 at 16.02
To: CCP4 bulletin board 
Subject: Postdoc position in Structural Data Science at NNF-CPR at the 
University of Copenhagen (Taylor and Rasmussen groups)

Dear all,

We are looking for a joint postdoc in “Structural Data Science” in the Taylor 
group (Structural Biology of Molecular Machines) and Rasmussen group (Human 
Proteome Variation) at the Novo Nordisk Foundation Center for Protein Research, 
University of Copenhagen. We aim to recruit a scientist with extensive 
experience in data science and/or in silico protein folding or design to help 
pioneer and establish this new research field. The position is for 2 years in 
the first instance and can be renewed for up to 4 years in total, providing a 
unique long-term opportunity to work on an exciting project in a well-equipped 
and supportive environment. The position is available immediately, start date 
will be decided together with the candidate.

The full advert and link to the application form can be found here: 
https://employment.ku.dk/faculty/?show=154452

Please contact me (nicholas.tay...@cpr.ku.dk) 
or Simon (simon.rasmus...@cpr.ku.dk) directly 
for further enquiries.

Application deadline:  16 August 2021, 23.59pm CET

Best wishes,

Nicholas

Nicholas M. I. Taylor, PhD
Associate Professor

University of Copenhagen
Faculty of Health and Medical Sciences
Novo Nordisk Foundation Center for Protein Research
Blegdamsvej 3B, building 6.1
2200 Copenhagen N
Denmark

nicholas.tay...@cpr.ku.dk
http://www.cpr.ku.dk

[cid:image001.gif@01D78EE4.725EC4A0] [cid:image002.png@01D78EE4.725EC4A0] 






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Re: [ccp4bb] convert loop into a sheet

[Matthew Snee]

Is it not just a case of adding "beta sheet restraints" in the real-space 
refine options menu?

If it goes back to a loop during refinement then that may mean that the atomic 
positions don't meet the requirements?

Get Outlook for Android

From: CCP4 bulletin board  on behalf of rohit kumar 

Sent: Wednesday, August 11, 2021 5:41:55 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] convert loop into a sheet

Hello Everyone,

I was trying to build my peptide (8 AA long) as ligand in coot. Peptide should 
be in the form of Sheet, after multiple cycles of refinement peptide still in 
the loop form. If anyone could help me, how to convert this loop structure into 
a sheet in coot , would be very helpful?
I am using ccp4-Refmac5 for the refinement.


Thank you
Rohit




--
Regards
Dr. Rohit Kumar Singh






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[ccp4bb] convert loop into a sheet

[rohit kumar]

Hello Everyone,

I was trying to build my peptide (8 AA long) as ligand in coot. Peptide
should be in the form of Sheet, after multiple cycles of refinement peptide
still in the loop form. If anyone could help me, how to convert this loop
structure into a sheet in coot , would be very helpful?
I am using ccp4-Refmac5 for the refinement.


Thank you
Rohit




-- 
Regards
Dr. Rohit Kumar Singh



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[ccp4bb] Experienced crystallographer needed

[Mooers, Blaine H.M. (HSC)]

Dear all,

Please share this job announcement with potential candidates.


Associate Director of the Laboratory of Biomolecular Structure and Function

The Laboratory of Biomolecular Structure and Function (LBSF) at the University 
of Oklahoma Health Sciences Center (OUHSC) seeks an experienced 
crystallographer to run the daily operations of the LBSF. The position is at 
the Assistant Professor of Research level. The candidate will be responsible 
for working with PIs to advance their structural biology projects. These 
efforts will include routine technical operations, developing new protocols to 
overcome challenging problems, and training the staff of user labs in protein 
purification, crystallization, data collection, and structure determination. 
The ideal candidate for this position will have a PhD and ten years of 
experience in macromolecular crystallography. The candidate will not be 
expected to write grant applications. Pluses in a candidate's background 
include experience with membrane protein purification and LCP crystallization,  
experience with Cyro-EM, or experience with other structural biology methods.

The LBSF is part of a suite of core labs supported in part by the OUHSC Vice 
President of Research. The LBSF is also part of the Biomolecular Structure Core 
(BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural 
Biology (OCSB), which is based on the main campus in Norman.  The BSC has 
contributed to the awarding of 23 million dollars in grant funding and 33 
publications in the past nine years. The OCSB has been the focal point of 
Oklahoma's structural biology community for nine years. The community includes 
50 labs at three major research institutions.

The BSC will be a vital part of a new Center for Therapeutic Science. The 
center will coordinate and foster the drug development pipeline with the BSC 
playing a central role in structure-based drug design. Most of the 12 major 
users of the LBSF have cancer-related projects. One project led to the 2021 
publication of crystal structures of RET Kinase bound to two drug molecules 
recently approved by the FDA for the treatment of non-small cell lung cancer. 
Most of the major users are members of the Stephenson Cancer Center, a National 
Cancer Institute-designated cancer center.

The compensation level for this full-time position includes a generous benefits 
package. The position is based in Oklahoma City -- an affordable place to raise 
a family. To apply, please submit a cover letter, CV and contact information 
(name and email) for three references to Blaine Mooers, Director of the 
Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at 
ouhsc.edu. The position will remain open until filled. Application review will 
begin immediately.

OUHSC is an equal opportunity employer and is committed to creating a diverse 
and inclusive environment for all employees.



Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Office: 405-271-8300 Lab: 405-271-8312 

Websites:
Faculty page: 
https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): 
https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology


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[ccp4bb] Postdoctoral Research Associate (Halic lab)

[Bilokapic, Silvija]

Dear all

We seek a highly motivated postdoctoral research associate to join the group of 
Dr. Mario Halic in the Department of Structural Biology at St. Jude Children's 
Research Hospital.

The Halic lab studies the epigenetic regulation of gene expression using 
genetics, molecular biology, biochemistry and structural biology approaches. In 
particular, we study heterochromatin formation and the chromatin-modifying 
proteins involved in this process. We use cryo-EM methodologies to examine 
processes involved in chromatin organization and also apply genetics and 
molecular biology approaches to investigate heterochromatin formation in 
fission yeast. More information about the lab, publications and ongoing 
projects can be found here: https://www.stjude.org/research/labs/halic-lab.html

We seek an independent researcher with a PhD and strong background in molecular 
biology and genetics/epigenetics or in biochemistry and structural biology to 
join our group. Preference will be given to applicants who have received their 
Ph.D. degree within the last 3 years.

This is an excellent opportunity for an early-career scientist to broaden their 
skill set. You will join a vibrant community at the Department of Structural 
Biology at St. Jude Children's Research Hospital, with access to 
state-of-the-art facilities that enable integrative structural biology and 
biophysics investigations, including cryo-EM, X-ray crystallography and NMR, 
single-molecule imaging, protein-protein interactions, combined with 
computational and data-science approaches. More information about the 
department can be found here: 
https://www.stjude.org/research/departments/structural-biology.html

St. Jude Children’s Research Hospital has a highly collaborative research 
environment, with numerous institutional shared resources and core facilities. 
In addition, postdocs benefit from excellent salary and benefits package: 
https://www.stjude.org/education-training/advanced-training/postdoctoral-fellows/funding-benefits-for-postdocs.html


Applicants should submit CV and cover letter (describing research experience 
and interests) and names and addresses for 3 references to 
mario.ha...@stjude.org.


Follow us @LabHalic





Silvija Bilokapic, PhD

Structural Biology

St. Jude Children’s Research Hospital

262 Danny Thomas Place

Memphis, TN 38105-3678





Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer



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[ccp4bb] Protein Scientist Position at Affinivax

[Heidi Burke]

Dear all,

I am searching for a Protein Scientist to join my team at Affinivax to
contribute to the development of many types of vaccines. The full job
posting can be found here:

https://affinivax.com/careers/

Email me directly if interested.

Many thanks,
Heidi



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