On 11/05/2022 22:28, Kenneth Satyshur wrote:
I have a disulfide bond defined in the pdb as SSBOND. It shows up in coot as a link between the sulfur atoms. But when I use 'sphere refine' the link is broken and there is no disulfide bond.


That doesn't sound right. How close are the SG atoms?


The same happens for my CYS  to ZN ligands.


That's completely different.


They are defined with a 'LINK' line in the pdb.


OK. So coot should use the metal restraints then.


How do I tell 'sphere refine' to not break these links? Do I need to define a restraint explicitly?


You shouldn't need to - it should do the right thing. But it seems like it isn't doing so in this case - that sounds like a bug.


Paul.


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