Dear Mr.:

        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.

        In fact,what I am doing now is to model a protein which has a hign homology with another protein of which the structure has been known.The template is thermophilic and has a disulfide bond.The target has two cys amino acids in the same places where the template form the disulfide bond.However,after the target model has been established,the Chimera software indicate that no disulfide bond exists.The target protein has no ability of thermostability.So I want to use the MODELLER software to explore the differences between them and find out what factors influence the target protein and make it can't be thermophilic.The disulfide bond is the first element I  take into account.

        How do I solve the problems above?

        I am very appreciate your advises.

                                                                                         Yours sincerely,

                                                                                          Rao    Ben