Re: [modeller_usage] Regarding Model Building

[Modeller Caretaker <>]

On 04/22/2012 02:17 AM, Ashish Runthala wrote:
> I have a pretty small question. Is there a way in MODELLER where i
> can completely use a single template along with its side-chain
> topology?

Where you have a 1:1 alignment, the initial model is exactly the same as 
the template. If you don't want Modeller to optimize this, you can 
override select_atoms():

http://salilab.org/modeller/9.10/manual/node23.html

> In normal modelling scripts, it simply harness the peptide backbone
> localization information from the template and then fixes the
> side-chains with its own algorithms.

No, the initial model is simply copied from the template where the atom 
names are the same (this usually means the backbone and part of the 
sidechain, depending on the type of the aligned residue). Side chain 
dihedrals are not strongly restrained though, so during optimization 
they can certainly move from these initial positions.

	Ben Webb, Modeller Caretaker
--
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