Re: [modeller_usage] reproduction

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

On 7/4/11 5:57 AM, Jean-Paul Armache wrote:
> how to inform modeller to reproduce this part, of just the whole
> protein which as little deviation as possible (ie. to closely
> resemble the template) ?

If you want it to look *exactly* like the template, you can simply 
unselect this part of the protein:
http://salilab.org/modeller/9.9/manual/node23.html

(This will only work, of course, if you have 100% sequence identity in 
this region, or can supply a good starting model.)

Otherwise, you can ask Modeller to include more restraints, which will 
more tightly constrain the target backbone to resemble the template. 
This was discussed recently:
http://salilab.org/archives/modeller_usage/2011/msg00268.html

Of course, this will only work if you have reasonable sequence identity 
between target and template. If the identity is very low, then you will 
probably have a hard job building a good structure using comparative 
modeling in any case.

	Ben Webb, Modeller Caretaker
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