Dear BIN ZHANG,
MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete.
However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues.
Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes.
The story continues until the number of iterations are over.
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
Message: 1
Date: Sun, 8 Apr 2012 23:58:13 -0700
From: BIN ZHANG <>
To:
Subject: [modeller_usage] In what are the initial structures
different?
Message-ID: <>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Dear All:
I have a question about the differences of the initial structure built
for homology modeling. Can anyone tell me how exactly are these
initial structures different? Do they differ in the secondary
structures in uncertain regions? I cannot find this information in the
manual.
For example, by using
a = automodel()
a.starting_model = 1
a.ending_model = 50
I can built 50 different homology models starting from different
initial structures, but I have want to know how these different
initial structures are constructed.
Thanks very much for help.
Best,
Bin