[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:



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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