Sergio Garay wrote:
My name is Sergio Garay and I am pretty new using modeller so it is probable that my questions can be "a little" silly. I am trying to build a model with two kind of restrictions (using a multiple templates alignment): a disulphide bridge and the position of ligands. I was able to obtain (following your tutorial) models with each restriction applied in a separate way. The problem appear (errors) when I try to combine bothrestriction at the same time. I am using mod9v6, and I follow the examples ofthat version. Is there any problem in my py script?
The problem isn't that you are trying to do two things at once - the problem is actually a very simple one, reported by Modeller:
KeyError: 'No such residue: 345'
i.e. there is no residue called "345" in your model. (In your Python script you're trying to set up a disulfide bond between residues 345 and 668.) Note that the residue numbers in the model are generally not the same as those in your template(s). The chain IDs may also be different (e.g. you may mean 345:A rather than 345). The easiest way to be sure is to do a simple run with the regular automodel class (without your MyModel modifications) and replace
a.make() with a.make(exit_stage=2)That will generate a single unoptimized model (.ini file). You can then inspect that model to see the residue numbering for future runs.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage