[phenixbb] Occupancies

[sbiswas2 at ncsu.edu]

Hi Amit,
I dont know which version of phenix you are using. I tried this recently
with the most recent version using command line. Refinement of alternate
conformation is in the default parameters of phenix. So just go to coot
add the alternate conformation to fit your density save your model and
then run the phenix refine from the command line. The output file has the
refined model with different occupancies of the atoms. I also tried this
with CNS but it does a poor job with occupancy refinement.Hope this helps.
Shya





> Hello
>         I am new to phenix. I am tring to refine the occupancies using the
> phenix.refine gui. In the refinement settings- refinement strategy :
> occupancies , when I define the groups for individual atoms as chain A and
> resseq 1:200 (for protein atoms) and a ligand group in constrained as
> chain
> B and resseq 1:10 and chain C and resseq 1:10, the refinement fails with
> several errors. The refinement runs fine when I do not touch the
> "occupancies" panel on the gui.
> How do I refine in Phenix the occupancies defining as well as partitioning
> the molecule as individual, groups and coupled groups?
>
> Thanks in advance,
> Amit
>
>
> --
> AMIT DAS,
> PROTEIN CRYSTALLOGRAPHY SECTION,
> SOLID STATE PHYSICS DIVISION,
> BARC, TROMBAY,
> MUMBAI-400085.
> INDIA.
> Alt E-mail:amitdas at barc.gov.in <E-mail%3Aamitdas at barc.gov.in>
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