�Ġ� wrote: > I have some questions about two commonds > model.patch_ss_templates() and model.patch_ss().First,I don't know what > exactly does these two commonds want to do.In my opinion,the earler can > indicate wether the disulfide bonds exist and where are they and the > later has the same function of which the target is the protein which is > modeled.But after I have run the commond and used the mdl.energy() > commond,I don't how to understant the output file.I don't know what > information I can get from the .log file.
See http://salilab.org/modeller/FAQ.html#3
model.patch_ss_templates() adds disulfide bonds to your model if you have a Cys-Cys pair aligned with a disulfide bond (determined by inter-residue distance) in the template. This is done automatically for you by the automodel class anyway.
model.patch_ss() adds disulfide bonds for every Cys-Cys pair in your model, if they are sufficiently close. But this is probably not suitable in your case.
model.patch() is used to manually add disulfide bonds, is probably what you want, and is described in the example at the link provided above.
Ben Webb, Modeller Caretaker