Hi Fred,
I don't know about Discovery studio but I know in Pymol you can select the
peptide ligand yourself, e.g. via a sequence view. It just depends on what type
of analysis you are doing.
Joel
-Original Message-
From: CCP4 bulletin board On Behalf Of Fred Vellieux
Sent: Monday, July 3, 2023 10:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question about BIOVIA DiscoveryStudio 2021
Folks, apologies for the non-CCP4 software question.
I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my
browser does not allow me to open their "contact form".
I am trying to visualize and perform an analysis on a protein:smaller molecule
complex. The smaller molecule happens to be a long peptide.
Whatever I do with the PDB (change ATOM cards to HETATM, change residue names
to PEP, UNK, LGD, introduce MODEL and ENDMDL cards) DiscoveryStudio indicates
the input PDB file doesn't contain any ligand.
Would any one in this community have an idea of how to specify that a part of a
coordinate file is the ligand, so that DiscoveryStudio 2021 recognises it as
such and allows me to proceed?
Thanks,
Fred.
--
MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic
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