The following script optimize.py is not working for me. It is giving an error in the line: is giving an error in this line:
env = environ() env.edat.dynamic_sphere = True
code = 'unbound-scrwl' aln = alignment(env) mdl = model(env, file=code) aln.append_model(mdl, align_codes=code, atom_files=code) aln.append_model(mdl, align_codes=code+'-ini', atom_files=code+'.ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file=code+'.ini')
# Generate the restraints: mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) mdl.restraints.write(file=code+'.rsr')
mpdf = mdl.energy() mdl.switch_trace(file=code+'.trc') mdl.optimize(optimization_method=1, max_iterations=20, output='REPORT', trace_output=1) mdl.optimize(optimization_method=3, temperature=300, max_iterations=50, output='REPORT', trace_output=1) mdl.optimize(optimization_method=1, max_iterations=20, output='REPORT', trace_output=1) mpdf = mdl.energy()
Dr. Jayashree RamanaLecturer, Department of Biotechnology and Bioinformatics Jaypee University of Information Technology Waknaghat, Solan Himachal Pradesh-173234
On 04/22/2011 03:34 AM, email@example.com wrote: > The following script optimize.py is not working for me. It is giving an > error in the line:
It would be more helpful if you said what the error was - then I wouldn't have to guess! But it looks like this is an extremely old script, for Modeller 8. If you're using Modeller 9 (I would recommend that) then you will need to be some adjustments to it. See http://salilab.org/modeller/9.9/manual/node255.html for a suitable script.
BTW, if you are looking to do "serious" optimization, this script probably isn't going to be up to the task.
Ben Webb, Modeller Caretaker