Re: [modeller_usage] Loop modeling while restraining the secondary structure

[Modeller Caretaker <>]

On 01/24/2011 09:48 PM, bharat lal wrote:
> The number of residues that has to be
> mentioned for restraining should according to the target sequence only
> know ?? ..

I think you are asking how to number your residues. Modeller always uses 
model numbering, not the residue numbers or chain IDs from your template(s).

> Also, I generated some 5 models while restraining some portion of the
> sequence as beta strands and after seeing all the structures I found
> that its model 3 that is having perfectly restrained beta sheets as
> compared to others but its DOPE score is more as compared to other
> structures . In this type of situation how do we have to select the
> correct model ??

How you choose your "best" model is up to you. The best DOPE score is 
not necessarily the best model - it is not a perfect scoring function.

> Also, I would like to ask one more thing about restraining structure
> that while giving the residue range generally last 2 or some times 1
> residue/s doesnot retain the restrained structure .. In that case what
> do i need to do ??

You will have to experiment. You may need to modify your alignment.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage