[phenixbb] excluding atoms from refinement

Jeff Headd jjheadd at lbl.gov
Thu Dec 8 10:29:27 PST 2011

Hi Crystal,

You can exclude any part of your model with a selection like this:

refinement {
  refine {
    strategy = *individual_sites *individual_sites_real_space rigid_body \
               *individual_adp group_adp tls *occupancies group_anomalous
    sites {
      individual = "not chain B"
      torsion_angles = None
      rigid_body = None

In this example, I've excluded chain B from individual site
refinement. You can see more selection examples here:



On Thu, Dec 8, 2011 at 10:21 AM, Crystal VanderZanden
<Crystal.Vanderzanden at colostate.edu> wrote:
> Does anybody know if there a general code that will allow us to exclude
> something from refinement?  I would like to specify that there is a
> particular part of my structure that I don't want to refine the position.
> I've thought about deleting those atoms from the pdb file, but then that
> phasing information is excluded from the refinement.  Any ideas?
> Thanks,
> Crystal
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