[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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