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## model.patch_ss() -- guess MODEL disulfides from model structure

`patch_ss()`

> This command defines and patches disulfide bonds in MODEL using MODEL's current structure. A disulfide bridge is declared between all pairs of Cys residues whose SG-SG distances are less than 2.5. The covalent connectivity is patched accordingly.

> This command should be run after model.read() and before optimization to ensure that the disulfides are fixed properly and that no SG-SG non-bonded interactions are applied.

> topology.submodel is needed to make sure the correct atomic radii are used in CYS-CYS patching.

Example: See model.patch_ss_templates() command.