[phenixbb] pdbtools: how to set the occupancy for an atom selection?

Pavel Afonine pafonine at lbl.gov
Mon Apr 13 08:20:34 PDT 2015

Hi Alex,

Phenix GUI -> Model tools -> PDB Tools -> Options -> click on 
Occupancies -> in popped up window type in atom selection and choose one 
of three available actions (randomize..., set..., reset...) -> hit OK -> 
hit Run.

I think that should do it.

In the command line:

phenix.pdbtools model.pdb occupancies.set=0.46 selection="chain A and 
resseq 1:2"


On 4/13/15 6:46 AM, Alejandro Virrueta wrote:
> Hello,
> I was wondering if someone could show me a way to set the occupancy of 
> a specific set of atoms to 0 using phenix.pdbtools.
> I noticed here 
> <http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html#anch2> that 
> there is no option under modify => occupancies to do an 
> 'atom_selection'. Any help would be appreciated.
> Cheers,
> Alex

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