Folks,
I am using Mod8v1 on a MAC G5 running OSX 10.3. In a protein with about 500 aa there was about a 100 amino acid region which did not match the single available template. I asked Modeller to make 1000 loops in the gap region. The happened and after a few fits I got the DOPE analysis of all 1000 loops complete. I picked the best 20 loops (lowest overall DOPE scores;minimal plots in the loop region) and examined these structures. In every one of the best twenty AND in the worst loop model, I see regions where the routines have threaded the loop though the nonloop regions of the original model. In words, suppose I have two antiparallel beta sheet strands. The backbone of the loop sometimes passes between these sheet stands or through the turn loop at the ends of the sheets before coursing away from the existing protein.
Do the loop generator routines pay any attention at all to the nonloop regions?
In older versions of Modeller, the routines would create knots where the insertions in the alignment were present. The alignment could be adjusted to prevent this.
How can I persuade modeller not to thread regions of loop through "existing" non loop regions of the protein?
Starr