I'm working on a project that studies the effects of the alignments
on the quality of the 3D models produced by modeller. basically I'll
be using heuristics to iterativevly refine the alignment and hence
result in a better 3D model by Modeller. My question is what's the
simplest alignment method used by modeller that can produce me
alignments between a target and a single template? and how would I
see this alignment? how would I access it? for example there is this
method: automodel.auto_align(). is this the simplest alignment
producing function or there are other ways to produce weaker
alignments? and how would I get a hold of this alignment produced by
the function (in this case automodel.auto_align())?
The simplest way to use it would be to modify the example at that URL
for your inputs, and use it to generate the .ali file that you then feed
to automodel.