Re: [modeller_usage] how satisfactory relative orientation of modeled domains can be achieved in two matches cases

[Modeller Caretaker <>]

On 01/25/2011 04:32 AM, Maria Persico wrote:
> I am exploring ModBase to build a model for the REcQ2 of arabidopsis
> Thaliana(swiss prot acc: Q9FT73).
> ModBase found 2 structures matching this target and after downloading
> the coordinates file and also the showfile.chimerax file, I was able
> to visualize with chimera both structures with apparently a
> satisfactory relative orientation. Below I copy-paste the target
> coverage:
>
> 		2v1xA 	(63-592) 	crystal structure of human recq-like dna helicase
> 		1wudA 	(531-602) 	e. coli recq hrdc domain
>
> I wanted to know if there is an optimization step in the ModBase
> pipeline to achieve this and if it is referenced somewhere...

ModBase just uses Modeller to build its models - it is not doing 
anything special. In fact, those two models are built entirely 
independently - they are not aligned or oriented. So the orientation 
you're seeing is entirely arbitrary - it depends on how the two template 
structures are oriented.

	Ben Webb, Modeller Caretaker
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