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 > o.kgosis...@usask.ca -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
signature.asc
Description: Digital signature
