[modeller_usage] What is a difference between automodel and loopmodel with respect to refining only part of the model optimization ?
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Subject: [modeller_usage] What is a difference between automodel and loopmodel with respect to refining only part of the model optimization ?
From: "Mahesh Velusamy" <>
Date: Thu, 7 Jul 2016 22:04:32 +0530 (IST)
Dear All,
Let me explain that what I have tried:
I have generated 100 models for one single point mutation sequence
following optimization(loop model) on single point mutated residue along
with neighbour residues(with different sphere range 1A°-10A°). Now, the
observation from my out put is as following:
1. When i optimized the SPM model with the large sphere (10A°) of
neighbour residues, I got bad model compared to crysal structure but DOPE
score was really high(~5K).
2.When i optimized the SPM model with the less sphere (1A°) of neighbour
residues, I got similar model compared to crysal structure but DOPE score
was really bad(~250).
So , I dont understand why I am getting less DOPE score when I have
similar good models compared to crystal structure and vice versa.
Then, I followed the same procedure but automodel default optimization on
selceted region where i got all the models simlar to crystal structure
with less difference between dope score(range ~5k to 6K)
Now, I want to what is the difference between automodel and loopmodel
optimization on selected region ? and what loop model optimization exactly
does ? and why there is a illogical contrast between DOPE score in loop
model optimization?
Thanking you in advance
With Regards
Mahesh V