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. thanks, Shya
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.