Re: [modeller_usage] Modeling with multiple templates

[Modeller Caretaker <>]

On 6/12/10 3:47 PM, sdh wrote:
> I want to model a big fibrous protein using several templates. The
> templates do not overlap (gap is no longer then 1-3 residues) or overlap
> over few residues.
>
> I found the following sentence in the FAQ: "If no additional information
> is available about the relative orientation of the two domains the
> resulting model will probably have an incorrect relative orientation of
> the two domains when the overlap between A and B is non-existing or
> short. To obtain satisfactory relative orientation of modeled domains in
> such cases, orient the two template structures appropriately before the
> modeling."
>
> My questions are: how precisely the templates have to be oriented? Would
> be cursory placing enough?

Orientating the templates will only affect the initial (unoptimized) 
model. Since there are no constraints on the domain-domain interaction, 
the final (optimized) model may not respect that orientation. So you 
would obtain better results if you can add simple additional restraints 
between the domains:
http://salilab.org/modeller/9v8/manual/node27.html

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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