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@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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