[phenixbb] How to define a disulfide bond between symmetry related molecules in phenix.refine
Pavel Afonine
pafonine at lbl.gov
Wed Feb 25 08:37:26 PST 2015
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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