Re: [ccp4bb] Coot crashes when delete side chain

Thanks Nick, Michael, Engin and others for sharing the insight. Indeed it did not crash but was only hidden. I can restore the window and keep it there by clicking the “keep delete active” box. So far it works fine. Thanks, Jinhua From: Nicholas Clark Date: Tuesday, March 7, 2023 at 7:21 PM

[ccp4bb] wwPDB News: PDB entries with extended CCD or PDB IDs will be distributed in PDBx/mmCIF format only

Dear all, As announced previously, wwPDB, in collaboration with thePDBx/mmCIF Working Group , has set plans to extend the length of accession codes (IDs) for PDB and Chemical Component Dictionary (CCD) entries in the future. PDB entries containing these

[ccp4bb] postdoctoral researcher position at University of Minnesota

Dear all, An immediate postdoctoral research associate position is available at Dr. Wei Zhang's laboratory at the University of Minnesota, Twin Cities, USA. The successful candidate will lead experimental design and execution to investigate the structural transformation of enveloped viruses

Re: [ccp4bb] Structural alignment and classification

This sounds suspiciously like what the team from EBI that Eugene and I have been working with either have done, or want to do. They already have a way to cluster structures, but GESAMT is overfitting for their needs. It might not for yours, but it would depend on exactly what you want to do.

Re: [ccp4bb] Running Refmac from WinCoot

Hi, I haven’t encountered these issues, however I am routinely using CCP4i2 on Windows 10. A fresh install of CCP4 Program Suite v8.0.009 + SHELX + COOT v0.9.8.1 (exe) has worked well. After Refmac5, I use the button “Coot” to launch a new task, then run WinCoot from there. When I use

Re: [ccp4bb] Rational mutations and crystallizability

maybe this can help too: https://pross.weizmann.ac.il/step/pross-terms https://proteopedia.org/w/Journal:Molecular_Cell:1 best, Bruno ### Bruno P. Klaholz Centre for Integrative Biology Department of Integrated

Re: [ccp4bb] Rational mutations and crystallizability

Sorry/Correction, the link I send is apparently also obsolete: The page is still accessible but no jobs can be submitted. Workaround might be, use XtalPred-RF and use the information/outcome for guidance to mutate your protein sequence of interest…... Best J. -- Dr. math. et dis. nat. Jeroen

Re: [ccp4bb] Structural alignment and classification

yes selecting models and chains in SSM & Gesamt is possible -- Eugene From: CCP4 bulletin board on behalf of Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: 06 March 2023 14:55 To: ccp4bb Subject: Re: [ccp4bb] Structural alignment and

Re: [ccp4bb] Structural alignment and classification

Having indeed written Gesamt some 10-12 years ago, I had to refresh my memory before answering. Gesamt definitely aligns multiple structures, just give them all on command line. It should do clustering in "sheaf" mode (which assumes that chains have same lengths and atoms are matched

Re: [ccp4bb] Rational mutations and crystallizability

https://services.mbi.ucla.edu/SER/intro.php Best J. -- Dr. math. et dis. nat. Jeroen R. Mesters https://orcid.org/-0001-8532-6699 University of Lübeck Institute of Biochemistry https://www.biochem.uni-luebeck.de phone: +49-451-3101-3105

[ccp4bb] Rational mutations and crystallizability

Dear All, I remember that 10-15 years ago there was at least one website predicting/suggesting residue mutations potentially able increase crystallizability of a protein. I recall, for example, http://www.doe-mbi.ucla.edu/Services/SER but it is not working any longer. Some of the sites

Re: [ccp4bb] Coot crashes when delete side chain

You can also use the Command key plus the tilda ~ to toggle through the active windows of a current application (so you need to still be in XQuartz). I’ve found this to be the quickest way to get back to the main Coot window. Alice -- Alice Dawson Structural Biologist Division of Biological

[ccp4bb] Helping improve AlphaFold DB - survey on similarity searches

** *Dear list, * * The AlphaFold Protein Structure Database (https://www.alphafold.ebi.ac.uk ) team are excited to announce plans to expand the database’s capabilities, and we need your help with it. We seek feedback on how you perform protein similarity