On 4/26/13 2:17 AM, Anogna wrote: > I have been struggling from past one week with the following kind of > modelling.... > > I have a target sequence which is 97% identity with two PDB's (named A > and B) > I just want to make A as main template, but A has some residues missing, > so i thought of making B as template for those missing residues in the > "PDB A". > > But to go with this I am not able to get a python script file in which i > can specify build residues.

This sounds straightforward. You wouldn't do anything special in the Python script, but you would craft an alignment to use the B template only in the regions where A is deficient. See questions 1 and 2 in the FAQ: http://salilab.org/modeller/9.11/FAQ.html

Ben Webb, Modeller Caretaker