next up previous contents index
Next: build Up: The model class: handling Previous: model.patch_ss_templates() guess   Contents   Index

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

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 2.5Å. The covalent connectivity is patched accordingly.

This command should be run after 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.

Ben Webb 2008-05-05