On 02/09/2015 09:36 AM, Mouses Stamboulian wrote: > 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 alignment is alignment.align(): http://salilab.org/modeller/9.14/manual/node306.html
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.
Ben Webb, Modeller Caretaker