[phenixbb] set_biso_to_wilson_b gone?
pafonine at lbl.gov
Sun Aug 5 10:14:11 PDT 2007
> I've just noticed that in the last version of PHENIX (1.3b-d7) this is
> not recognised anymore:
> refinement.modify_start_model.adp.set_biso_to_wilson_b = true
> is this intentional?
I'm afraid, yes. There are some technical reasons for this. You still
have at least two ways of doing this:
1) When running phenix.refine :
% phenix.refine data.mtz model.pdb modify_start_model.adp.set_b_iso=xxx
where xxx is Wilson B values (that you may get from previous
phenix.refine runs; phenix.refine reports it).
2) We recently added a tool for PDB file(s) manipulations. Currently it
is very simple but will grow based on needs and user's requests.
For example, it can read in a model and for selected or all atoms:
- modify ADP (randomize, shift, set to a value, scale, convert to/from
- modify sites (shake, apply rotation / translation);
- modify occupancies;
- remove selected atoms;
- write out a PDB file with modified model.
To get started type: phenix.pdbtools -h
I'm attaching a copy of a quick manual for phenix.pdbtools (it will be a
part of new updated PHENIX documentation).
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