Dear Sir/madam, 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. 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". And could I model three loops at the same time? Thanks. Ester
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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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ESTER FUSTE DOMINGUEZ -
Modeller Caretaker