[phenixbb] .cif use/restraints

Pavel Afonine PAfonine at lbl.gov
Tue Dec 15 18:20:45 PST 2009

Hi Bryan,

- check the .cif file to make sure it defines the ideal geometry that 
you are expecting from your ligand to have;

- check .geo file to see if the restraints for that particular ligand 
are actually used in refinement. The .geo file contains the list of all 
the geometry restraints used in phenix.refine refinement (bonds, angles, 
planarities, chiralities, dihedrals, non-bonded, NCS, custom defined 
restraints and edits), for each and every atom, making it a complete 
foot-print of geometry restraints used to obtain the final refined 

- is your ligand located on a special position?


On 12/15/09 6:03 PM, Bryan W. Lepore wrote:
> a ligand is distorting - as if it is ignoring the .cif and i already 
> have the angles tighted up in the .def.  what else should i check?
> what i did :
> generated some elbow output.  the .cif was provided to phenix.refine 
> on cmd line.  the .pdb had the H's and CONNECT's removed, but the .cif 
> retains them.  the .pdb was incorporated into a single .pdb input file.
> -bryan
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