alignment for multiple chain modelling
Hello,
For multichain modelling (ex. for a hetrodimer), Is it possible to force the alignment program in modeller to choose particular chain for the alignment?. For example use only template A chain for 1st chain in the sequence and template B chain for 2nd chain in the sequence.
env = environ() aln = alignment(env) mdl = model(env, file=3gsn, model_segment=("FIRST:A, "LAST:B)) aln.append(file='seq.ali', align_codes='seq') aln.align2d() aln.write(file=align.ali, alignment_format='PIR')
Thanks for any leads.. Sal
On 8/26/15 1:26 PM, thanj sal wrote: > For multichain modelling (ex. for a hetrodimer), Is it possible to force > the alignment program in modeller to choose particular chain for the > alignment?. > For example use only template A chain for 1st chain in the sequence and > template B chain for 2nd chain in the sequence.
If your template and target both have two chains, and the chains are of similar length in template and target, then another way of thinking about this is that you want Modeller to align the chain breaks (/) in target and template. It should do this automatically, controlled by the break_break_bonus parameter: http://salilab.org/modeller/9.15/manual/node306.html
If your template and target are of dramatically different lengths, or have different numbers of chains, then note that by default the alignment is global, so won't probably won't do what you're hoping for.
Ben Webb, Modeller Caretaker
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thanj sal