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Hi Joel,
If you fixed an existing restraint file you can send it to the CCP4 support staff preferably with a description of what was changed and why. A PDBid for a structure model with that particular compound (for testing) is also very welcome. New compounds will end up in the dictionary eventually, but this will and should only happen once the containing structure is released by the PDB. It is very likely atom names will change during the annotation process to make them more consistent with existing compounds (e.g. modified amino acids and carbohydrates have specific naming schemes).
HTH,
Robbie
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Joel Tyndall
Sent: Monday, November 10, 2014 05:46
To: [log in to unmask]
Subject: [ccp4bb] Small molecule cif files
Hi all,
If a crystallographer determines a liganded structure of say a new small molecule. Where does the cif file come from when the next version of ccp4/phenix gets released. Along the same lines. If a cif file is not quite correct (or were not parsed against the CSD) and is subsequently updated by an individual. Is there a process for updating existing ligand cif files?
My reason for the question is around several ligand complexes that we have had to generate new cif files in order to get the correct conformational parameters (centred around unsaturated rings)
Regards
Joel
_________________________________
Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
Ph: +64 3 479 7293