[phenixbb] linking only one conformer to a thiol

[Nigel Moriarty]

Chris

Can I have the model or at least the two residues involved.

Cheers

Nigel

---
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 Thu, Apr 5, 2018 at 5:13 PM, Krzysztof Bzymek <kbzymek at gmail.com> wrote:

> Hi,
>
> I'm trying to refine a structure with a disulfide bond between a cysteine
> and a thiol-containing peptide. There are two conformations for the
> thiopeptide, in one of them the thiol is facing away from SG of the
> cysteine (~7 A away). I defined the link as:
>
> refinement.pdb_interpretation  {
>   apply_cif_link {
>     data_link = DRG-CYS
>     residue_selection_1 = chain A and resname DRG and resid 10
>     residue_selection_2 = chain B and resname CYS and resid 20
>   }
> }
>
> I also tried:
>
> refinement.pdb_interpretation  {
>   apply_cif_link {
>     data_link = DRG-CYS
>     residue_selection_1 = chain A and resname DRG and resid 10 and altloc A
>     residue_selection_2 = chain B and resname CYS and resid 20
>   }
> }
>
> After refinement (with a corresponding data_link.eff file defining the
> bonds and angles), the thiol of the other conformer that was facing away
> from the cysteine moves out of the electron density and now faces the
> cysteine (still about ~5.7 A away).
>
> Is there a way to define a link between only one conformer and have the
> other refine independently? I did try refinement without the above link
> definition (relying on the proximity of the two cysteines and automatic
> linking in phenix) but some of the bond and dihedral angles showed higher
> deviation from ideal values expected for disulfide bonds.
>
> Thanks,
>
> Chris
>
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