On 9/29/14, 1:22 PM, Anjela Manandhar wrote: > Hi, I am new to Modeller. Here, I am trying to add missing residues in > my PDB. My PDB has two chains A and B. I checked the tutorial and > mailing lists where they talk about PDB with single chain. So, how can I > get an .ali file for my protein and how should I label the residues to > be inserted.
It is the same but you add a chain break character ('/') between the chains in your alignment file. See http://salilab.org/modeller/9.14/manual/node29.html
Ben Webb, Modeller Caretaker