-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jim,
the chemical basis would be that the Zn connects to all four S atoms, and if they are indistinguishable, all Zn-S distances should be alike. But the S-atoms are not bonded to each other, hence they want to have as much distance from each other as possible. Since they are four, this makes them a tetrahedron. I am not aware of a more automated/ simpler way of turning the angles at the metal into restraints other than calculating the S-S distances with a pocket calculator, although that does not mean they do not exist. Cheers, Tim On 06/07/2013 11:56 AM, James Naismith wrote: > 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 <[email protected]> > wrote: > > 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/ iD8DBQFRsd7bUxlJ7aRr7hoRAqcQAKDzPOPsplrajE/SeFHZSoiJKBsemgCgpD5h 7W0/oip1XvLO/g0cSeThxcE= =TiZu -----END PGP SIGNATURE-----
