Creating CIF Files and Renaming Ligands

From: Ai Fen Chai
Date: 25 August 2011 03:36

Hi all,

I want to add 2 new ligands (that do not exist in PDB) to my structure. I generated the ligands from PRODRG. The problem is that both of the ligands have the same name DRG. After renaming the ligands in both PDB and CIF files, I always get this error message "CIF dictionary does not contain restraints" whenever I try to do refinement. Prior to renaming, both ligands were recognized by COOT when they were named DRG. So, the CIF files themselves are ok and it must be something to do with the renaming that is causing the error. I am wondering whether renaming the ligands has changed the CIF file subtly and causing COOT and other refinement programs to not read it right?

Cheers,

Ai Fen

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From: Nicholas Keep
Date: 25 August 2011 09:45

Did you rename the ligand in the CIF file as well?  It would be nice if the Prodrg interface allowed you to type in the name of the ligand you want in the CIF and PDB file.  Hopefully a global replace in your favourite text editor of DRG with LIG or whatever you want to call your ligand would work.  You would have to do that on the separate pdb and CIF files and then merge the two or more CIF files into one if you have more than one ligand.  I must admit to this being theory I have not tested it in practice.
Best wishes
Nick
--

Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX


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From: Ai Fen Chai

Hi all,

Thanks for the suggestions! Anyway, the problems have been fixed! When I edited the CIF files in a mac editor, the file formatting got changed, so a line feed became a carriage return and Coot does not like this as to it they appear to be different files.

The CIF files were fixed by using gedit on the old files on linux machine and
global replace with match case/whole word only option on. They now are recognized by COOT.

Ai Fen