[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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