[modeller_usage] how to evaluate 100 profiles?

[hori koshii <>]

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?

 

It will be so appreciated and thanks.

The items need to be updated in the loop are bolded in the following script.

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from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in
env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology
env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

# read model file
mdl = model(env)
mdl.read(file='EGPh.B99990001.pdb')
aln = alignment(env)
code = "EGPh"
# generate topology
aln.append_model(mdl, atom_files='EGPh.B99990001.pdb', align_codes=code)
aln.append_model(mdl, atom_files='EGPh.B99990001.pdb', align_codes=code+'-ini')
mdl.generate_topology(aln, sequence=code+'-ini')
mdl.transfer_xyz(aln)

mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='EGPh.profile',
                normalize_profile=True, smoothing_window=15)

----------------------------------------------------------------------------------------------------------------------------

 

EGPh.BL01220001.pdb  EGPh.BL01570001.pdb  EGPh.BL01920001.pdb
EGPh.BL01230001.pdb  EGPh.BL01580001.pdb  EGPh.BL01930001.pdb
EGPh.BL01240001.pdb  EGPh.BL01590001.pdb  EGPh.BL01940001.pdb
EGPh.BL01250001.pdb  EGPh.BL01600001.pdb  EGPh.BL01950001.pdb
EGPh.BL01260001.pdb  EGPh.BL01610001.pdb  EGPh.BL01960001.pdb
EGPh.BL01270001.pdb  EGPh.BL01620001.pdb  EGPh.BL01970001.pdb
EGPh.BL01280001.pdb  EGPh.BL01630001.pdb  EGPh.BL01980001.pdb
EGPh.BL01290001.pdb  EGPh.BL01640001.pdb  EGPh.BL01990001.pdb
EGPh.BL01300001.pdb  EGPh.BL01650001.pdb  EGPh.BL02000001.pdb
EGPh.BL01310001.pdb  EGPh.BL01660001.pdb  EGPh.IL00000001.pdb
EGPh.BL01320001.pdb  EGPh.BL01670001.pdb  EGPh.BL01330001.pdb  EGPh.BL01680001.pdb

 

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