Andrew Leslie made a similar suggestion for using CB to S distances. Both make me unhappy for the reason that there is not a clear chemical basis to them (Tim's has more a chemical basis) and how would I choose the distance. (I can measure it from a known structure)
I have previously experimented with Tim's (works). I am searching for anyone who knew a simple way to restrain metal ion geometry in remfac based on angles at metal. best Jim On 7 Jun 2013, at 10:14, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > -----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 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 >>> >> > > - -- > 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-----
