how to generate the ini file only
Hello all,
Does anyone know how to ask modeller to generate the ini file and stop?
I tried the following but failed:
a = automodel(env, alnfile='my_alignment.ali', > knowns='3mrb', sequence='query', > assess_methods=assess.DOPE) > aln = alignment(env) > aln.append(file='T3mrb_Q1duz.ali') > a.transfer_xyz(aln)
Best,
Li
Ok, find the solution: > > > a = automodel(env, alnfile='T3mrb_Q1duz.ali', > knowns='3mrb_AP', sequence='query_1duzAC', > assess_methods=assess.DOPE) > aln = alignment(env) > aln.append(file='T3mrb_Q1duz.ali', align_codes=a.knowns+[a.sequence]) > a.make_initial_model(aln)
On Thu, Feb 6, 2020 at 4:44 PM Li Xue me.lixue@gmail.com wrote:
> Hello all, > > Does anyone know how to ask modeller to generate the ini file and stop? > > I tried the following but failed: > > a = automodel(env, alnfile='my_alignment.ali', >> knowns='3mrb', sequence='query', >> assess_methods=assess.DOPE) >> aln = alignment(env) >> aln.append(file='T3mrb_Q1duz.ali') >> a.transfer_xyz(aln) > > > Best, > > Li > >
On 2/6/20 7:44 AM, Li Xue wrote: > Does anyone know how to ask modeller to generate the ini file and stop?
Sure, set exit_stage=2 when you call a.make(). See https://salilab.org/modeller/9.23/manual/node69.html
Ben Webb, Modeller Caretaker
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Li Xue -
Modeller Caretaker