[phenixbb] Real-space refinement fails to restrain CYS SG ZN properly
Pavel Afonine
pafonine at lbl.gov
Mon Mar 2 16:57:44 PST 2020
Hi Aaron,
could you please send two model files: before and after refinement, and
indicate problematic residues?
Thanks,
Pavel
> I'm trying to refine a structure containing ZN bound to four cysteine
> residues.
> 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...
>
> phenix-1.17.1-3660/modules/chem_data/mon_lib/list/mon_lib_list.cif
>
> 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.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20200302/63fd8104/attachment.htm>
More information about the phenixbb
mailing list