[phenixbb] Real-space refinement fails to restrain CYS SG ZN properly
nwmoriarty at lbl.gov
Mon Mar 2 15:49:45 PST 2020
What version of Phenix?
Can you share the model (directly) with me?
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Mar 2, 2020 at 3:23 PM Aaron Oakley <aarono at uow.edu.au> wrote:
> I'm trying to refine a structure containing ZN bound to four cysteine
> I have had trouble with Real-space refinement mangling the residues around
> this ZN.
> At first, Real-space refinement tried to turn the cysteine into disulfides.
> I tried switching this off with…
> resname CYS and name SG
> …in the *disulphide bond exclusion selection string* under the *Model
> interpretation* menu (there are no disulfides in the protein).
> But the cysteine-zinc cluster continued to be mangled. Inspection of the *.geo
> file* shows that the SG-ZN distance is being restrained, but the CB–SG–ZN
> angle is not.
> I checked the relevant dictionary file...
> And the correct bond and angle restraints do seem to be present:
> ZN-CYS 1 ZN 2 SG single 2.340 0.020
> ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000
> Suggestions on how to fix this welcome.
> phenixbb mailing list
> phenixbb at phenix-online.org
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb