hori koshii wrote: > Hi, does anyone know python and modeller very well and give us some > help to run a model evaluation script for 100 homology models. (how > to set 'EGPh.B99990001.pdb' as a variable and make it like a loop so > the number can be increased by 1 in the next run), or another other > ways you know?
Assuming your models are named EGPh.B99990001.pdb through EGPh.B99990100.pdb, the following should do the trick, building profiles EGPh-1.profile through EGPh-100.profile:
from modeller import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') env.io.atom_files_directory = './:../atom_files'
for n in range(1, 101): # read model file mdl = model(env) code = "EGPh" file = '%s.B9999%04d.pdb' % (code, n) mdl.read(file=file) aln = alignment(env) # generate topology aln.append_model(mdl, atom_files=file, align_codes=code) aln.append_model(mdl, atom_files=file, align_codes=code+'-ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='%d-%d.profile' % (code, n), normalize_profile=True, smoothing_window=15)
Ben Webb, Modeller Caretaker