Hi, Thanks for the help regrading model-loop-define.py script. I have one doubt in model selection .. The number of residues that has to be mentioned for restraining should according to the target sequence only know ?? .. 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 ?? Here's the list of energies that I got : >> Summary of successfully produced models:Filename molpdf DOPE score GA341 score----------------------------------------------------------------------target.B99990001.pdb 1552.05176 -25341.12891 1.00000target.B99990002.pdb 1485.22974 -25387.23438 1.00000target.B99990003.pdb 1559.28723 -25382.83984 1.00000 (perfectly restrained str.)target.B99990004.pdb 1483.82568 -25213.86523 1.00000target.B99990005.pdb 1402.83508 -25525.49023 1.00000
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 ?? After doing the restrained modeling is it required to do loop refinement .. as I am doing loop refinement also by generating some 50 structures and then finally selecting the one with low DOPE score .. Is this strategy right or wrong ??
-------------- Bharat