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
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