[phenixbb] Occupancy issue

Simon Kolstoe s.kolstoe at ucl.ac.uk
Tue May 15 04:49:54 PDT 2012


Thanks Pavel,

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).

Thanks,

Simon


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?
> 
> 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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