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