[phenixbb] anisotropic refinement and hydrogens in coot.
mcollins at convex.hhmi.columbia.edu
Tue Aug 19 19:06:14 PDT 2008
I had been think of asking a friend to write a short python script
that could list all residues or even all atoms (below a user defined
B factor threshold) in a phenix selection format. Then I could run
this and just cut and paste the residues with ADPs below 5, or 10 or
20, and run phenix.refine with anisotropic for these differing
selections. The trick s getting someone to spend the hour or two I
need. Any takers? :-D
On Aug 19, 2008, at 6:05 PM, Pavel Afonine wrote:
> 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
> 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
> 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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