Dear Oarabile M. Kgosisejo,
if you add distant restraints between the metal and the oxygens, the side chains
should not be pulled into the centre.
I think that refmac5 recognises the LINK records in the PDB file, e.g. with the
syntax
LINK ZN ZN A2666 SG CYS A 102 1555 1555 2.41
I am not sure this holds true for phenix.refine. If not you need to define the
distance in the .eff file of your refinement, but I wouldn't know the syntax
without looking at the documentation at www.phenix-online.org.
Best,
Tim
On Fri, Mar 06, 2015 at 06:17:59PM +0000, Kgosisejo, Oarabile wrote:
> Hello all,
>
> I am refining the structure of a metalloenzyme with 2 Mn, a cacodylate and 5 residues coordinating the metal center (the active site) using 2.25 A data. I am able to place the residues in their electron density using Coot. However, after refinement using Phenix the metal-coordinating residues and the cacodylate molecule move out of their electron densities (they pull towards the metal center). Please see attached screenshot. The rest of the molecule is fine
>
> The edits and cif files used in refinement were created using Phenix ReadySet. The refinement options checked in Phenix are XYZ coordinates, Real space, Individual B-factors and Occupancies. X-ray/ stereochemistry and X-ray/ADP weights are optimized.
>
> I am wondering if there is refinement strategy or anything that I can do to keep the residues in the electron density?
>
> Your suggestions are appreciated
>
> Best Regards,
>
> Oarabile M. Kgosisejo
> [log in to unmask]
--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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