[phenixbb] tls refinement

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Mon May 11 12:50:31 PDT 2009

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
>> scale?
> 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!
> Pavel.

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