On 7/7/16 9:34 AM, Mahesh Velusamy wrote: > Now, I want to what is the difference between automodel and loopmodel > optimization on selected region ?
The difference is primarily in the scoring function used. In unaligned regions, automodel uses basically just the CHARMM forcefield. In aligned regions, automodel adds in information derived from the templates.
loopmodel uses the CHARMM forcefield plus a statistical potential. It totally ignores template information.
> and what loop model optimization exactly does ?
https://salilab.org/modeller/9.17/manual/node494.html
> and why there is a illogical contrast between DOPE score in loop > model optimization?
Your results look reasonable to me. Remember, DOPE score is an energy so lower values are "better".
Ben Webb, Modeller Caretaker