[phenixbb] anisotropic refinement and hydrogens in coot.

Pavel Afonine pafonine at lbl.gov
Tue Aug 19 08:25:01 PDT 2008

Hi Mark,

> 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."?

Yes, at 1.6A resolution you should refine anisotropic ADP. You can 
manually select atoms which you want to refine as anisotropic and isotropic:

phenix.refine model.pdb data.mtz params.par

where "params.par" file contains these lines (edited copy-paste from all 
parameters file):

refinement.refine {
    adp {
      individual {
          isotropic = (chain A and resseq 1-20) or (chain B and resseq 
          anisotropic= (chain A and resseq 234:426) or (chain B and 
resseq 765:900)

Currently phenix.refine does not allow to do selection on atomic 
properties, like B-factor values. So, you need to figure out yourself. 
As a start, I would just do this and see if it results in any problems 
(I think it will work just fine):

refinement.refine {
    adp {
      individual {
          isotropic = element H or element D or water
          anisotropic= not (element H or element D or water)

which tells to refine all atoms as anisotropic except water and 
hydrogens (deuteriums if any).

> 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.

phenix.refine can handle both the PDB V2 and V3 hydrogen atom names. 
Since Coot does not with the PDB V3 conventions, you can do everything 
with PDB V2 hydrogen names. If you use phenix.reduce to add the 
hydrogens, use the -OLDpdb option.


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