On 07/15/2010 06:07 AM, rsachdeva@imtech.res.in wrote: > I have built a homology model of my protein using a single template sharing 38% > sequence identity. Some of the functionally important residues of target protein > are conserved in the template. These residues are well aligned in the input > sequence alignment file. In the top most model so obtained, I found difference > in side chain dihedral angles of such identical residues. Since both target as > well as template contain a few identical residues, their secondary structure is > also same, then why these conserved residues in the model adopt rotamers > different from those of the template.

Modeller does not exactly preserve the structure of residues, even when they are identical to the template, since they may need to move due to structural changes in nearby residues. So it's entirely possible that you'll see deviations in sidechain dihedral angles, particularly if there's a conflict of restraints.

If you want to prevent some part of the model from moving at all (in which case, if the residues are identical to the template, they will stay that way) see http://salilab.org/modeller/9v8/manual/node23.html

Ben Webb, Modeller Caretaker