Hi Shya,

here is an example of PDB file that has plenty of alternative conformations:

http://www.rcsb.org/pdb/files/1ejg.pdb

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.

Pavel.

On 5/11/09 12:50 PM, [email protected] 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.
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.