On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote:
> Just a remark/precaution: if you remove ANISOU records then you will
> basically invalidate the refinement results (the refined model).
If that is true then I would say there is a deeper problem.
The description of the TLS groups in the header records should be
sufficient to regenerate the ANISOU records when needed. If this
is not already the case, then I suggest that we, as a community,
need to work out how to make it the case and then lobby for that
solution to be mandated by the PDB.
But I think it's not that bad. I have had good results from reproducing
the reported R factors from the TLS header records plus the ATOM records.
Admittedly, the PDB files I used for testing were refmac refinements
rather than phenix refinements.
> Make
> sure you recompute the R-factors after removing ANISOU and be prepared
> to see (much) higher values.
Well, that depends on what program[s] you use to recalculate the R values.
If you actually use the TLS information in the header records then it
should come out close to the original values.
Ethan
> Pavel.
>
>
> On 6/30/10 11:09 AM, Nat Echols wrote:
> > On Wed, Jun 30, 2010 at 10:59 AM, Pavel Afonine <pafon...@lbl.gov
> > <mailto:pafon...@lbl.gov>> wrote:
> >
> >> I am refining a structure at 2.25 A using Phenix.refine. I am
> >> using TLS parameters for refinement but as i use TLS, phenix does
> >> individual anisotropic refinemnt also.
> > No, it doesn't: it does not do "individual anisotropic refinement"
> > unless you specifically asked for this.
> >
> >
> > It does, however, print out individual ANISOU records at the end of
> > refinement - but these are extracted from the TLS groups, not refined
> > individually. If you absolutely must get rid of them, "grep -v ANISOU
> > refined_file.pdb > new_file.pdb" will do the trick, but personally, I
> > always like to look at the ellipsoids in PyMOL or Coot anyway, to see
> > what the TLS groups are doing.
> >
> > -Nat
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
