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 structure. - is your ligand located on a special position? Pavel. 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb