Hi all, Thank you very much for your suggestions. Refmac5 took care of the problem. I really appreciate your comments
Best Regards, Oarabile M. Kgosisejo o.kgosis...@usask.ca ________________________________ From: Pavel Afonine [pafon...@gmail.com] Sent: March 6, 2015 2:07 PM To: Kgosisejo, Oarabile Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Residues won't stay in electron density This should do it (if not please get back to me off-list with sending data and model files): Refinement settings -> Ligand linking , then Options->Link metals . phenix.refine does not trust anything in PDB file header except CRYST1 records. Pavel On Fri, Mar 6, 2015 at 10:17 AM, Kgosisejo, Oarabile <o.kgosis...@usask.ca<mailto:o.kgosis...@usask.ca>> 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<mailto:o.kgosis...@usask.ca>
