[phenixbb] tls refinement
PAfonine at lbl.gov
Mon May 11 13:58:19 PDT 2009
here is an example of PDB file that has plenty of alternative conformations:
FYI: the letters A,B,... in front of residue names are altloc
identifiers that mark alternative conformations - this is exactly what
that slide shows.
Normally, you either create residues in alternative conformations either
manually or using a corresponding option in COOT. Of course, you need to
see the justifying density for them.
On 5/11/09 12:50 PM, sbiswas2 at ncsu.edu wrote:
> Hi Pavel,
> Thanks for the slides.
> I tried running using default parameters however the output pdb had all
> atoms with occupancy 1. How do I put atloc identifiers its not clear in
> the slide.
>> Hi Shya,
>>> my question now is why is the R value high without the anisotropic
>> goto: http://www.phenix-online.org/presentations/neutron_japan_2009/
>> and click on "Structure refinement and PHENIX (morning session) (PDF)".
>> The slides number 19-21 will answer your question. Please let me know if
>> it's still not clear.
>>> Second question is:
>>> can I refine alternate conformations using the command line or is it
>>> already there in the default parameters?
>> Yes, phenix.refine automatically does constrained occupancy refinement
>> for atoms in alternative conformations. All you need for this is to have
>> altloc identifiers in input PDB file.
>> See slide #38 in the above link for example.
>> Please let me know if you have any questions!
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