[phenixbb] DTT mediated disulfide crosslink across a crystallographic two-fold! (Pavel Afonine)

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Aug 4 12:03:57 PDT 2010

Hi Joe,

> Thanks Pavel! I will wait and see what Ralf says regarding defining
> the symmetry operator.

In Coot, switch on drawing symmetry atoms. When you click on a symmetry
atom coot will tell you in the bottom line which atom it is and which
symmetry operator was used to draw it. Enter this symmetry operation
the way Pavel described before.

> If I am using the GUI for phenix.refine should
> I create a new file with the bond definition you mention and include
> it as one of the starting files or should I edit the Refine_*.eff
> file that gets created and insert it somewhere there?

You could edit the eff file, but I believe it is easier to make
a seprate new file with the custom bond definitions.

BTW: sorry before I hadn't realized that your disufildes were
not between two CYS. phenix.refine only finds CYS-CYS disulfides


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