[phenixbb] Occupancy issue
s.kolstoe at ucl.ac.uk
Tue May 15 04:49:54 PDT 2012
So if I turn on the overall occupancy strategy and then set the occupancies of the atoms I want to refine at 0.9 it works. HOWEVER it also refines the occupancies of atoms on a different chain that I want to fix at 0.5 (I have a ligand that crosses a symmetry axis). So what command do I use to turn off the occupancy refinement for the other chain? Is it something like:
occupancies.remove_selection = chain Y
(from the phenix.refine documentation page).
On 15 May 2012, at 10:56, Pavel Afonine wrote:
> 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?
> 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+
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