Prabhakar. G. wrote: > am modeling a homo trimer, from a homo trimer template, > each chain(A,B,C) in both template and query has 390 residues, > no gaps in the sequence alignment, and sequence identity is 64%, > but when the model is built , all the three chains in the models > are not having same secondary structural in certain parts, > eg: residues 15-24 is a strand in A chain and B chain but it is a coil > in C chain. > Is there a way to preserve the secondary structure in all the chains of > the models?

http://salilab.org/modeller/FAQ.html#12

> and why does this change of secondary structure happens? > There are no such secondary structure variations as far as > the template chains are concerned.

Modeller combines information from your templates with a physics-based force field and statistics, and tries to fulfill all restraints. Your template secondary structure is only one of many restraints, and thus may not be preserved, particularly as the sequence identity decreases.

Ben Webb, Modeller Caretaker