[phenixbb] B-factors

Pavel Afonine pafonine at lbl.gov
Thu Aug 5 15:37:21 PDT 2010

  Using the command line this would look like:

phenix.pdbtools model.pdb set_b_iso=20 selection=water


On 8/5/10 10:04 AM, Nathaniel Echols wrote:
> On Thu, Aug 5, 2010 at 7:53 AM, Hermella Woldemdihin 
> <hermifi at yahoo.com <mailto:hermifi at yahoo.com>> wrote:
>     Where can I set B-factor for water in phenix.refine on the GUI
>     version of phenix?
> Do you mean resetting the B-factors for all waters, or the B-factor 
> for new solvent molecules when the water picking option is selected? 
>  For the latter, it is here:
> Settings menu->Ordered solvent...->Initial B-factor value
> (You may need to change the "user level" menu to "intermediate" or 
> "advanced" if you don't see that control at first.)
> If you want to reset B-factors for existing waters, open Settings 
> menu->Model modifications->Modify ADPs, enter the selection for waters 
> in the first control ("resname HOH" is usually all you need), and 
> enter a suitable value in "Set isotropic B to:".
> Of course in either case, by default phenix.refine will re-refine 
> those initial values.
> -Nat
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