-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear James,
I am not sure I fully picture what your coordination looks like, but my guess is that if you include distance restraints between the S-atoms you can distinguish between a tetrahedral geometry and a square pyramid. You could use external restraints in refmac - just make a dummy run with prosmat to get the syntax right and copy and modify a few lines tailored to your problem. Best, Tim On 06/07/2013 10:39 AM, James Naismith wrote: > 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 [email protected] > > 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 <[email protected]> > 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: [email protected] >> >> 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 [email protected] >>> >>> 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 >> > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRsaSGUxlJ7aRr7hoRAqILAJ9JlBpeDHpxvQYthbuftvdtySxgXACfXHzM 2T2XGXN7Kjxo6NtXv/XefwU= =S75X -----END PGP SIGNATURE-----
