[phenixbb] Check for radiation-induced reduction of a disulfide bond

Pavel Afonine pafonine at lbl.gov
Sat Feb 13 08:28:03 PST 2016


> I'm working with one protein, crystallized in oxidized form, which 
> exhibits negative density in the Fo-Fc map at the center of the 
> disulfide bond. As a test of radiation-induced reduction during data 
> collection, I'd like to do a trial refinement described in a previous 
> work from literature, where SG sulfurs of involved cysteines were 
> refined without van der Waals interactions to monitor distances of 
> these atoms.
> How can I do this calculation in Phenix? Thanks in advance

specifically what repulsions you want to disable (between what atoms)? 
Note, if SG is involved in disulfide bond then there is no repulsion 
term between it and the other SG.

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