[phenixbb] Help with a Cd(2)Cl(4)O(6) cluster
Pavel Afonine
pafonine at lbl.gov
Mon Nov 1 16:40:36 PDT 2010
Hi John,
here is what I would do (I hope Nigel suggests a better approach):
option 1: create a PDB file with this construct using Coot, and make
sure the geometry is approximately correct. Then try
phenix.ready_set cluster.pdb
to obtain a CIF file defining ideal geometry. Make sure the CIF files
defines the geometry the way you expect it (inspect it visually or using
REEL).
option 2: threat these atoms as a bunch of independent atoms and use
phenix.refine to define restraints:
http://phenix-online.org/documentation/refinement.htm#anch84
(in addition to what's listed in the link above - custom restraints for
bonds and angles, you can also define the planarity restraints).
Pavel.
On 11/1/10 12:36 PM, John Rose wrote:
> Hi,
>
> I have a Cd(2)Cl(4)O(6) cluster in my structure and would like to set-up constraint files for it PHENIX. Any help here would be appreciated.
>
> O Cl Cl Cl O
> . . . . .
> . . . . . .
> . . . . . .
> O . . . Cd Cd . . . O
> . . . .
> . . . .
> . . .
> O Cl O
>
>
> Thanks,
>
> John
>
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