[phenixbb] Question about antibumping restraints and restraints on dihedrals

Madhumati Sevvana; Biotechnik msevvana at biologie.uni-erlangen.de
Wed Aug 22 03:07:26 PDT 2007

I could successfully refine a merohedral twin in phenix.refine but I have
a few unanswered questions:
1. Is there a way of applying antibumping restraints to decrease the
number of clashes in phenix.refine, I looked at older posts but couldn't
get a satisfactory guideline regarding the same.
2. The default setttings for geometry refinement looks like this:
refinement.geometry_restraints.remove {
  angles = None
  dihedrals = None
  chiralities = None
  planarities = None
Do I have to change "dihedrals=True" if I do not want to put restraints on
dihedrals. I was thinking that one puts restraints on psi/phi angles only
by setting "discard_psi_phi = False" because when I set it to
"discard_psi_phi = True", the Ramachandran plot was much better. But I did
not want to do this because then the Ramachandran plot is no more a
validation tool. I just wanted to know if Unknowingly I did that by
setting up "dihedrals = None".
Thank you in advance.

Madhumati Sevvana, PhD
Lehrstuhl fuer Biotechnik
Henkestr. 91, D-91052
Erlangen, Germany

Tel: 0049-9131-8523083
Email: msevvana at biologie.uni-erlangen.de

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