Thanks for this other suggestions similar (see below.) My problem is not the distances per se, these restrain fine to 2.3A
I am relatively low resolution and my problem is with just distance restraints I move to a square planar arrangement. I suspect this is a feature of the geometry restraints dominating refinement (c'est la vie at low res). I do not force Zn to be anything (the cif file just has a distance) I think. What I need to do is create another restraint someone how that imposes a Td geometry. What I cannot figure how to do is set this up because it involves 5 residues (4 cys and 1 Zn). best Jim Jim Naismith BSRC, North Haugh j...@st-andrews.ac.uk 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 On 6 Jun 2013, at 16:11, Roger Rowlett <rrowl...@colgate.edu> wrote: > 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: rrowl...@colgate.edu > > 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 >> j...@st-andrews.ac.uk >> >> 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 >
