Dear Anat,
Replying on behalf of Chris Thorpe:
The only reliable way I've found is to compare the conformations in each
of the biological units and also to look for ALTLOCs. Obviously you can
automate all of this, using BioPandas to compare peptide conformations
(looking at position level RMSDs) and having some BioPython/Pymol code
to deal with ALTLOCs and split them into different files.
Hope that helps!
Kind regards,
Deborah
On 24/06/2024 10:31, Anat Bashan wrote:
Dear CCP4 community,
I am interested in searching in the PDB for ligands that are in
complex with proteins in the PDB that were deposited with a double
conformation.
Does anyone know how to run such a search? How to define it?
Thanks a lot for your help,
Anat.
=========================================================================
Anat Bashan , Ph.D Tel:972-8-9344289 <tel:972-8-9344289>
Senior staff scientist @The Ribosome Group
The Weizmann Institute of Science
The Department of Chemical and Structural Biology Mobile:972-52-3347229
Rehovot 7610001 e-mail:
anat.bas...@weizmann.ac.il <mailto:anat.bas...@weizmann.ac.il>
Israel
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
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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