[ccp4bb] Postdoc @ Sanofi in Cell Line Development

2023-02-01 Thread Saurabh Sen 
Dear Community,

We are recruiting a postdoc, if you happen to know of any interested
candidates please feel free to pass along:

https://sanofi.wd3.myworkdayjobs.com/SanofiCareers/job/Framingham-MA/Postdoctoral-Fellow---Cell-Line-Development_R2678533-1

Best regards,
-Saurabh



-- 
Dr. Saurabh Sen
Asso Director, Cell Line Development
Sanofi USA

Cell: 608-609-4858



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[ccp4bb] Problems displaying CCP4i2 remotely on Mac with CCP4 8.0

2023-02-01 Thread Chris Richardson 
Hi,

We have a team who run all their CCP4 jobs on a central server, displaying the 
CCP4i or CCP4i2 GUI remotely on a Mac laptop or desktop using XQuartz and ssh.

With the update to CCP4 8.0, CCP4i2 now crashes.  The issue appears to be 
rendering the GUI via ssh on X11.  There are a variety of errors, including


QQuickWidget: Failed to make context current

QOpenGLShader: could not create shader

and


Failed to create OpenGL context for format QSurfaceFormat(...

This is not the problem often experienced with remote X11 sessions of iGLX not 
being permitted - coot from 8.0 runs, as do other GL applications.

As far as I can tell, this is because the GUI uses features of GL2.0+.  
Indirect GLX only supports GL up to 1.4.

If anyone has this working, any help they can give would be greatly appreciated.

Chris

--

Chris Richardson | Scientific Computing - Division of Structural Biology

The Institute of Cancer Research | 237 Fulham Road, London SW3 6JB

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[ccp4bb] Structure Predictors: Use ModelCIF for Computed Structure Models

2023-02-01 Thread Deborah Harrus 

Dear all,

ModelCIF (GitHub ) is a data 
information framework developed for and by computational structural 
biologists to describe structural models of macromolecules derived from 
computational methods. It provides an extensible data representation for 
deposition, archiving, and public dissemination of these models of 
proteins to enable delivery of Findable, Accessible, Interoperable, and 
Reusable (FAIR) data to users worldwide.


A. Overview of the ModelCIF extension of PDBx/mmCIF. B. Schematic 
representation of ModelCIF data specifications. ModelCIF includes 
definitions for input data used in template-based and template-free 
modeling; reference information for macromolecular sequences and small 
molecule components; local and global CSM quality metrics; and metadata 
information regarding modeling protocol, CSM classification (ab initio, 
homology, etc.) and descriptions of associated files. 
/A. 
Overview of the ModelCIF extension of PDBx/mmCIF. B. Schematic 
representation of ModelCIF data specifications. ModelCIF includes 
definitions for input data used in template-based and template-free 
modeling; reference information for macromolecular sequences and small 
molecule components; local and global CSM quality metrics; and metadata 
information regarding modeling protocol, CSM classification (ab initio, 
homology, etc.) and descriptions of associated files./


ModelCIF is an extension of the Protein Data Bank 
Exchange/macromolecular Crystallographic Information Framework 
(PDBx/mmCIF ), which is the global data 
standard for representing experimentally-determined, three-dimensional 
(3D) structures of macromolecules and associated metadata. The 
PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by 
the wwPDB in collaboration with relevant community stakeholders such as 
thewwPDB ModelCIF Working Group .


This semantically rich and extensible data framework for representing 
computed structure models (CSMs) accelerates the pace of scientific 
discovery. Furthermore, use of this data standard promotes 
inter-operation among structural biology data resources, with ModelCIF 
currently used by theModelArchive 
,AlphaFold DB 
, andMODBASE 
repositories. A manuscript was 
recently submitted to/bioRxiv/ 
describing the architecture, 
contents, and governance of ModelCIF as well as tools and processes for 
maintaining and extending the data standard [1].


Visit theModelCIF GitHub for more 
information about this data information framework.


[1] Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, et al. ModelCIF: 
An extension of PDBx/mmCIF data representation for computed structure 
models./bioRxiv/doi:10.1101/2022.12.06.518550 
.



Read this news on the wwPDB website: 
https://www.wwpdb.org/news/news?year=2023#63d28b2c314f0e7e1b1d3ce6



Kind regards,

Deborah Harrus

PDBe

--
---
Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Enhanced Collection of Starting Models

2023-02-01 Thread Deborah Harrus 

Dear all,

A new PDBx/mmCIF category, _pdbx_initial_refinement_model has been 
introduced to improve information collected about starting model for 
X-ray, 3DEM and NMR methods.


Experimentally derived vs computed models will be distinguished. 
Provenances of the resources where the starting model was obtained 
(e.g., PDB, AlphaFoldDB, RoseTTAFold, etc.) and its accession 
code/identifier will be captured, if publicly available.


For the full definition, see pdbx_initial_refinement_model>. An example 
is below:


_pdbx_initial_refinement_model.id 1
_pdbx_initial_refinement_model.entity_id_list 1
_pdbx_initial_refinement_model.type 'experimental model'
_pdbx_initial_refinement_model.source_name PDB
_pdbx_initial_refinement_model.accession_code 3LTQ

wwPDB strongly recommends all PDB users and software developers to 
review their code and adopt this definition for future applications.


Read this news on the wwPDB website: 
https://www.wwpdb.org/news/news?year=2023#63d97981c031758bf1c30fec


Kind regards,

Deborah Harrus

PDBe

--
---
Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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