On 09/11/2012 07:09 PM, Ashish Runthala wrote: > Is there a way that i can ask MODELLER to exactly copy the topology > of backbone,CA atoms of all the aligned residues and model the same > for the other unaligned loop chunks. But it should not add the side > chains. Is there a way that the side chain addition can be stopped > after the desired initial backbone, CA construction.

Modeller can build models using a variety of topologies. The default topology includes all heavy (i.e. non-hydrogen) atoms. You can change this by assigning to automodel.toplib. For example,

a = automodel(...) a.toplib = '${LIB}/top_mnch.lib' a.make()

will build a model containing only mainchain atoms.

You cannot mix topologies, however (for example, you can't build part of the model using all atoms, and part with just the backbone).

Ben Webb, Modeller Caretaker