On 01/09/2023 11:37, Guenter Fritz wrote:
Dear Paul,
I had a strange issue today when refining a structure with latest coot
(0.9.9.91) from CCP4.
Two cysteines with Calpha-Calpha distance of about 6 A do not form a
disulfide bond, but coot wants to enforce a disulfide, although no
disufide is defined in the pdb.
Does coot now automatically assume disulfides for Cys closer than a
certain distance?
Yes. Although I now believe that the linking code in Coot needs to be
completely reworked. When I started on this code, it was a sensible
idea not to trust the links and SSBONDS in the coordinates file, so Coot
worked them out itself. Today that is the wrong approach.
If yes, I guess there is a parameter that one can set?
Sadly no.
I do believe though that a recent fix will solve the problem.
I need to find some time to make a release. I'll try to do that next week.
The relevant commit is 7e2518b1452f18d011db43b57210bce71cfa41e5 if you
want to apply it yourself.
Paul.
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