Re: [modeller_usage] Loop refinement

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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