[phenixbb] anisotropic refinement and hydrogens in coot.

Mark Collins mcollins at convex.hhmi.columbia.edu
Tue Aug 19 07:51:30 PDT 2008

Two hopefully quick questions;

1) The phenix.refine documentation has a section 'Refinement at  
"higher than medium" resolution - getting anisotropic'.  I have a  
1.4A structure that clearly falls into this category, I've added  
riding hydrogens and now I'd like to try anisotropic ADPs.  Is there  
a way, to list all residues (preferably in phenix selection format)  
that have "relatively small isotropic B-factors ~5-20A**2 of so."?

2) The output.pdb file from phenix.refine is I think the pdb v3.0  
format.  Is there an option or apps to convert to v2.3, within phenix  
rather using remediator (duke)?  Coot still uses v2.3 files, which is  
fine until hydrogens are added to a pdb, because the nomenclature has  
changed.  RSR in coot causes these 3.0 named hydrogens to fly off the  
residue into surrounding density.

Thanks in advance, Mark

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