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