[phenixbb] How to define a disulfide bond between symmetry related molecules in phenix.refine

[Oleg Sobolev]

Hi Michael,

The SS bond should be established automatically if S atoms are closer then
3A to each other. If this is not the case for you, I am interested in
getting your .pdb file (or just the part with 2 residues in question) to
investigate this case.

Best regards,
Oleg Sobolev.

On Wed, Feb 25, 2015 at 8:37 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hi Michael,
>
> phenix.refine ignores PDB file header records (or most of them) except
> CRYST1, so adding SSBOND is not going to help.
>
> If this bond is not defined automatically (it should, normally) (you can
> check this by looking it up in .geo file that lists all restraints) then
> you can always define it manually using "Custom bonds" mechanism:
>
>
> http://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles
>
> Pavel
>
>
> On 2/25/15 2:03 AM, Michael Hothorn wrote:
>
> Dear all,
>
> I am trying to refine an intermolecular disulfide bond in phenix.refine.
> The disulfide involves Cys 188 in chain A and Cys 188 of chain B of a
> symmetry related molecule, with symop -X, Y+1/2, Z+1/2. There are two
> molecules in the AU, SG is P212121. I generated the following SSBOND entry
> in the pdb header:
>
> SSBOND 2 CYS A   188  CYS B   188                    1555  3555 2.04
>
> Based on this:
> http://www.wwpdb.org/documentation/file-format/format33/sect6.html the
> format seems fine, but the disulfide is not being recognized during
> refinement.
>
> Could someone point out to me how to correctly define this for
> phenix.refine.
>
> Thanks!
> Michael
>
>
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