[phenixbb] group_adp default ? and other phenix questions?

hari jayaram harijay at gmail.com
Tue Jun 17 12:44:22 PDT 2008

Hi I quite new to the phenix environemnt and just ran a phenix refinement
with the following command line

*phenix.refine  myfile.mtz  mymodel.pdb simulated_annealing=true model.ncs
refinement.main.ncs=true --overwrite
refinement.ncs.excessive_distance_limit=None  >phenix_06_18_2008_2.log *

The model.ncs file is structured as follows

refinement.ncs.restraint_group {
  reference = chain A
  selection = chain B
  selection = chain C
  selection = chain D

My data is good to 3.3 A ( membrane protein)  and thus far I have been
refining with refmac5. After the phenix run indicated above,  I had a
dramatic reduction in r/rfree  ( post refmac 33/36 AND post phenix 28/31).
This is despite relatively small changes to my model by the simulated
annealing refinement.

I have a few questions about the process and am hoping some phenix veterans
can help me out.

1) At my resolution I guess I should at best be refining only one B-factor /
ADP per residue is this the default behavior with the command line above

2) I have seen the emails about syntax for forcing group-B refinement at this
Basically they use strategy=group_adp . I am imagining this calculates one
ADP per residue or per defined group.  In my case if I force the behavior
with the syntax , how is group ADP for NCS-mates handled?

3) On a general note , when I say phenix.refine --show-defaults , the
section on strategy has a long list, what do the asterisks (*) in the syntax
mean .Does that mean those are the defaults .
Also how can I infer the syntax from this hierarchy?

Sorry for the long list of questions but I am very happy with phenix and
just thought I should understand the syntax better.
Thanks for your help
Hari Jayaram

phenix.refine --show-defaults returns

refine {
    strategy = *individual_sites rigid_body *individual_adp group_adp tls \
               individual_occupancies group_occupancies group_anomalous
    sites {
      individual = None
      rigid_body = None
    adp {
      individual {
        isotropic = None
        anisotropic = None
      group = None
      one_adp_group_per_residue = True
      tls = None
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