Re: [phenixbb] Occupancy issue

On Tue, May 15, 2012 at 2:27 AM, Simon Kolstoe wrote:

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+

You want "element CD", not "element CD2" - "CD2" is the residue name. -Nat