[phenixbb] Occupancy issue
Pavel Afonine
pafonine at lbl.gov
Tue May 15 02:56:08 PDT 2012
Hi Simon,
one of possible ways: just change the starting occupancy values to
something between 0 and 1, for example, set them to 0.9. That will be a
sign for Phenix to refine their occupancies.
Yours way should work too (though I don't know all the details,
including what's in .def file), but may be you try resetting occupancies
first?
Pavel
On 5/15/12 2:27 AM, Simon Kolstoe wrote:
> Hi phenixbb,
>
> I'm wanting to refine the occupancy for just a few Cadmium atoms in a structure but not refine any other occupancies. I've used the following command however the occupancies haven't refined:
>
> phenix.refine refinement_006.def occupancies.individual="chain X and element CD2"
>
> and the cadmiums are in the pdb file as:
>
> ATOM 8740 CD+2 CD2 X 1 -81.043 91.612 65.218 1.00 11.63 X CD2+
> ATOM 8741 CD+2 CD2 X 2 -78.111 92.072 62.948 1.00 11.15 X CD2+
> ATOM 8742 CD+2 CD2 X 3 -85.283 28.170 80.931 1.00 12.01 X CD2+
>
>
> Thanks,
>
> Simon
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