diff --git a/ScriptA.py b/ScriptA.py new file mode 100644 index 0000000..d7bd957 --- /dev/null +++ b/ScriptA.py @@ -0,0 +1,10 @@ +from modeller import * + +env = environ() +aln = alignment(env) +mdl = model(env, file='5NN8', model_segment=('FIRST:A','LAST:A')) +aln.append_model(mdl, align_codes='5NN8', atom_files='5NN8.pdb') +aln.append(file='gluc.ali', align_codes='gluc') +aln.align2d() +aln.write(file='alignment.ali', alignment_format='PIR') +aln.write(file='alignment.pap', alignment_format='PAP') diff --git a/scriptB.py b/scriptB.py new file mode 100644 index 0000000..1e4405a --- /dev/null +++ b/scriptB.py @@ -0,0 +1,18 @@ +from modeller import * +from modeller.automodel import * + +log.verbose() +env = environ() +env.io.atom_files_directory = ['.', '../atom_files'] + +a = loopmodel(env, alnfile = 'alignment.ali', + knowns = '5NN8', sequence = 'gluc') +a.starting_model = 1 +a.ending_model = 5 + +a.loop.starting_model = 1 +a.loop.ending_model = 2 +a.loop.md_level = refine.fast + + +a.make()