Mathew Smith wrote: > I was wondering how modeller uses the structural information of multiple > templates. > Are all aligned residues of all the templates used to create the restraints and > are they weighted in any way e.g. by sequence identity of template to target or > by residue type (exact matches weighted more than disimilar aa's)?

It uses all aligned residues in all templates and weights them using a function of local sequence similarity, distance from a gap, etc. See the 1993 paper for a full description.

> Also how can I alter these things so that I can tailor the restraints that I use > depending on in/dels and sequence similarity etc?

You have several options. You could override the functions that generate the restraints (see the build_charmm_restraints() and distance_restraints() methods in modlib/modeller/automodel/automodel.py), you could add and/or remove restraints after this is done, or you could manually edit the .rsr file.

Ben Webb, Modeller Caretaker