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