[phenixbb] Help with custom bond restraints syntax

Andrew T. Torelli att29 at cornell.edu
Tue Sep 29 08:54:12 PDT 2009

Hi all,

     I'm having what I believe is a simple problem defining custom bond
restraints between a side chain in my protein model and a ligand
(non-covalent bond).  Here is a minimal form of my custom bond
definition file that suffers from the error:

refinement.geometry_restraints.edits {
   Atom1  = chain F and resid 1 and name FE1
   Atom2  = chain A and resid 69 and name SG
   bond {
        action = *add
        atom_selection_1 = Atom1
        atom_selection_2 = Atom2
        distance_ideal = 2.35
        sigma = 0.1
        slack = None

     I'm using phenix 1.4-153 and I get the following error:
ERROR: Unused parameter definitions:
  refinement.geometry_restraints.edits.Atom1 (file
"/HOME/andrew/PHENIX_paramfiles/test.edits", line 5)
  refinement.geometry_restraints.edits.Atom2 (file
"/HOME/andrew/PHENIX_paramfiles/test.edits", line 6)

     I've checked through the online manual and I believe my syntax is
correct, but I'm not sure why my custom bond restraint is being

     A second question is: once I get the custom bond/angle restraints
correctly implemented, is there a better or more convenient place to
look and confirm that the restraints have been imposed other than the
.geo file phenix.refine outputs?

Thank you very much for your help,

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