[phenixbb] anisotropic refinement and hydrogens in coot.

Pavel Afonine PAfonine at lbl.gov
Wed Aug 20 00:03:36 PDT 2008

Hi Mark,

just to add to my previous email: you can easily change the script to be 
able to exclude the alternative conformations or hydrogen atoms or water 
(which you most likely want to do).


On 8/19/2008 7:06 PM, Mark Collins wrote:
> Hi
> 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
> Mark
> 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
>>> 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
>> automation).
>> 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.
>> Pavel.
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