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

["Mahesh Velusamy" <vmahesh@ibab.ac.in>]

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