[modeller_usage] is LOOP threading a common result?

[Starr Hazard <>]

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