[phenixbb] planarities definition help

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Oct 9 11:54:02 PDT 2007

Hi Partha,
Do you want to completely remove the restraints around the active site?
You can do that with this block in the parameter file:

  geometry_restraints.remove {
    angles = None
    dihedrals = None
    chiralities = None
    planarities = None

Where you see None, enter atom selections.
The restraints of the given type (angles, dihedrals, etc.) involving
the corresponding selected atoms will be removed.
You can have multiple lines for each restaint type.
You can check the result by inspecting the .geo file. It is a bit big,
but the atom labels are formatted exactly the same way as you see them
in your pdb file, e.g.
angle: (2, 1, 4)
  " C   LEU A 325 "
  " CA  LEU A 325 "
  " CB  LEU A 325 "
  angle_model: 110.834
  angle_ideal: 110.1
  weight: 0.277008
you can search for " C   LEU A 325 " in your pdb file or vice versa.
You could also try diff orig.geo mod.geo to check the effect of your

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