[phenixbb] set_biso_to_wilson_b gone?

Pavel Afonine pafonine at lbl.gov
Sun Aug 5 10:14:11 PDT 2007

Hi Luca,

> 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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