[phenixbb] ligand refinement

Christine Gee chrgee at gmail.com
Thu Feb 21 17:52:53 PST 2008

Dear Phenix developers
I have a covalently bound ligand in my structure and I would like to  
use phenix to refine the structure.  The ligand is bound to the  
sulfur of a cysteine.  What is the best method for defining the  
ligand.  Should I generate a cif file for the whole amino acid and  
the ligand, or can I make one for just the ligand and add in some  
restraint somewhere which tells phenix to make a bond between the  
ligand atom and a nearby sulfur in a cysteine.  If I generate a cif  
file with the whole amino acid and ligand, I assume I will I have to  
follow some convention in atom naming so that the main chain bonds  
and angles will form and refine OK?

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