delete SS link

[keitaroyam]

In the monomer library, the link SS (not disulf) is defined for any peptide residues having the "SG" atom. This is dangerous, because accidental SS links can be made.

SS . CYS-SS peptide . CYS-SS peptide SS-bridge

In the current library, there are 77 peptide monomers having SG atom, but only 03Y CG6 CYS DCY LE1 LEI are SS-linkable (others have C-S-C bonds for example).

I checked the "disulfide" connections from mmcif headers of the pdb entries including these monomers (apart from CYS), and found the following patterns. The DCY-DCY link is already defined as "Ddisul".

('DCY', 'DCY') 40 pdb
('CYS', 'DCY') 5 pdb
('CYS', 'LE1') 3 pdb

[GaribMurshudov]

It looks like a good idea.
In future we need to deal with the general links also

[GaribMurshudov]

In future, perhaps it would be good of @drlemmus would approve such changes. I would appreciate it very much if Robbie would agree to do this

[drlemmus]

This change was discussed previously on Discord. In general, yes, I can have a critical look before these sort of changes are made.

In future, perhaps it would be good of @drlemmus would approve such changes. I would appreciate it very much if Robbie would agree to do this