Re: [modeller_usage] Problem applying two different restrictions....

[Modeller Caretaker <>]

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 both
> restriction at the same time. I am using mod9v6, and I follow the 
> examples of
> that 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
--
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