[phenixbb] Select atoms by B-factors?

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Feb 24 19:17:32 PST 2009

Hi Oliver,

> I'm currently refining a structure at 1.6A. Substantial portions of  
> the structure are very well ordered, with B-factors < 15. I'd like to  
> refine these well ordered regions using anisotropic thermal  
> parameters, while keeping everything else isotropic. However, in doing  
> so, the atom selections tend to become quite convoluted. Is there any  
> way to select all atoms which initially have an isotropic B less than  
> a certain cuttoff value? That way one could (after isotropic B-factor  
> refinement) select the most ordered regions of the structure for  
> anisotropic refinement.

Direct selections like b < 15 don't currently work (good idea; added
to the to-do list), but you could try a trick. With some external
script, set the segid (columns 73-76) for the atoms you want to select,
e.g. BMIN, then use "segid BMIN" as the atom selection. If you have
non-blank chainids, I hope this will work.


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