[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] What is a difference between automodel and loopmodel with respect to refining only part of the model optimization ?

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
--
             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage