[phenixbb] anisotropic refinement and hydrogens in coot.

Pavel Afonine pafonine at lbl.gov
Tue Aug 19 15:05:49 PDT 2008

Hi Mark,

> After refinement with TLS how should we switch to 
> refinement with aniso individual ADPs. i know 
> that both cannot be done simultaneously at 
> present.

Just turn off the TLS refinement option. Since input PDB file will 
contain atoms with ANISOU records they will be refined as anisotropic 
automatically. Alternatively, you can specify which atoms to refine as 
isotropic or anisotropic.

> Following up on Mark's question: we also have a 
> set of structures of resolution 1.5 to 1.24 Å 
> resolution that are good candidates for 
> anisotropic refinement, but selecting the subset 
> of residues to refine is not easy (for us).
> We can  exclude loops and terminii with high 
> isotropic ADPs, but even for the remaining well 
> ordered parts of the protein we are left with 
> surface residues with well ordered main chain but 
> less well ordered side chains (e.g, Lys and Glu), 
> which need to be refined isotropically. Also, we 
> would like to exclude residues with alternative 
> conformations from anisotropic refinment.
> At present its a fair amount of work to build up 
> a residue selection to satisfy these requirements.

The goal is to make refinement completely automated where you hit Enter 
and get refined structure. What you describe above is one of the items 
in to-do list for further automation.

Also, I do not think you need to refine as isotropic the atoms with 
large B-factors. Yes, ac should probably be refined as isotropic. This 
is something to systematically study (as part of the overall planned 

For the moment, I would just remove from anisotropic refinement some 
very obvious parts that should be refined as isotropic and I'm almost 
sure it will be enough in most of the cases.


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