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Re: [modeller_usage] Loop refinement



ESTER FUSTE DOMINGUEZ wrote:
I built a model of a protein using Modeller, and with the PDB file obtained, I'm
trying to model loops. I follow the online manual instructions "refining an
existing PDB file". However, when I run mod9v2 I obtain this error:( "No such
residue: %s" % indx ) Key Error: no such residue 266.

Well, that's simple to understand - there is no residue called "266" in your model.

In the logfile I don't see what is wrong, and in PDB file 266 residue exists,
this is why I don't understand the error "no such residue 266".

You must be mistaken. Are you sure the residue doesn't have a chain ID, e.g. "266:A" ?

And could I model three loops at the same time?

Sure - the selection constructor can take multiple sets of atoms, e.g.

return selection(self.residue_range('1:', '10:'),
                 self.residue_range('20:', '30:'),
                 self.residue_range('40:', '50:'))

	Ben Webb, Modeller Caretaker
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