Hello Eleanor and Roger Rowlett and everyone, I am still having a tough time with coordinated metal refinements in refmac ( and coot )
I followed Rogers suggestion of creating a pseudo refmac run and then using the output cif definition for Cys -SG Zn as an input for further refinement. Even If I did input this cif , I see that my tetra-coordinated Zinc is pushed aside and my Cysteine SG - are disulphide bonded to each other creating a tetrahedral arrangement. One caveat . The Resolution of the data is no all that spectacular (2.5) so the whole assembly appears rather blobby with three clear Zn spheres like I would expect in the DELFWT maps before I model in the Zn. The other un-related problem is that coot seems to also want to bond Cysteines to each other when I do the real space refinement, but I think thats because SG-Zn restraints are not part of the coot dictionary .So the problem may very well be in the lack of a record in the pdb output by coot that says ..dont disulfide bond these Cys. I did check there were no explicit disulphide links defined or LINK or LINKR. So I am still nor refining these Cys-Zn links and have them mangled in my pdb, so any pointers will be greatly appreciated. Thanks for your help in advance Hari On Thu, May 13, 2010 at 12:50 PM, Eleanor Dodson <[email protected]> wrote: > Has anyone answered this? > Eleanor > > hari jayaram wrote: >> >> Hi >> >> Am trying to build coordinated Zn+2 by CYS -SG atoms and have it >> refine properly in refmac5.5 >> >> I added ZN ions in Coot at the Fo-Fc peaks. Then I defined manually >> the coordination relations in a text editor using LINK records. >> the ions were placed in the same chain that was doing the coordination. >> >> LINK ZN ZN A1001 SG CYS A 487 1555 1555 >> 2.34 >> >> I found that some of these ions refined well using refmac 5.5 and the >> resulting pdb had LINKR records in place indicating the coordinating >> interactions. >> >> For some of the Zn atoms however , the ions did refine , but coot >> still was covalently disulphide bonding the Cys to each other rather >> than coordinating the ZN and there were no LINKR records in the refmac >> refined pdb file. I know these interactions are legitimate because it >> is a known structure.Should I manually create LINKR records instead of >> LINK records after modeling in the ions? >> >> What is the correct procedure to model coordinating ions and have >> refmac treat them appropriately. >> Thanks in advance. >> >> Hari > >
