 |
 |
You can find instructions for restraining Zn-ligand distances here: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement&highlight=metal%20ion#Restraining_metal_ligand_distances_during_refinement_in_REFMAC Using this method, only Zn-ligand bond distances are restrained. REFMAC can usually find on its own certain Zn-atom linkages (I think it can find ZN-SG bonds with Cys by itself, but the version I am using usually misses or ZN-OD1 or ZN-OD2 bonds with Asp. This I pick up in the .cif file generated by REFMAC and include in a library file to be used for refinement. I have not had any issues with REFMAC altering ZN geometry. What you describe sounds like the geometry of the ZN atom has been defined or assumed somewhere in your approach. Cheers, _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [log in to unmask] On 6/6/2013 10:36 AM, James Naismith wrote: > I have a structure that I am trying to finish off, I have Zn ligated by four cys residues. > I use the linkR and define distances (the same link for each ZnS bond) > My issue is how to stop the structure moving to a square pyramid (consistent with distance restraints) rather than a tetrahedral geometry. > Can anyone help? > > best > Jim > > Jim Naismith > BSRC, North Haugh > [log in to unmask] > > Google scholar is free and tracks your outputs, mine are > http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMAAAAJ > > ResearcherID H-3408-2012; SCOPUS_ID 7005691850 > > http://www.researchgate.net/profile/James_Naismith/ > > The University of St Andrews is a charity registered in Scotland : No SC013532k