import pylab

import modeller

def get_profile(profile_file, seq):

"""Read `profile_file` into a Python array, and add gaps corresponding to

the alignment sequence `seq`."""

# Read all non-comment and non-blank lines from the file:

f = file(profile_file)

vals = []

for line in f:

if not line.startswith('#') and len(line) > 10:

spl = line.split()

vals.append(float(spl[-1]))

# Insert gaps into the profile corresponding to those in seq:

for n, res in enumerate(seq.residues):

for gap in range(res.get_leading_gaps()):

vals.insert(n, None)

# Add a gap at position '0', so that we effectively count from 1:

vals.insert(0, None)

return vals

e = modeller.environ()

a = modeller.alignment(e, file='TvLDH-1bdmA.ali')

template = get_profile('1bdmA.profile', a['1bdmA'])

model = get_profile('TvLDH.profile', a['TvLDH'])

# Plot the template and model profiles in the same plot for comparison:

pylab.figure(1, figsize=(10,6))

pylab.xlabel('Alignment position')

pylab.ylabel('DOPE per-residue score')

pylab.plot(model, color='red', linewidth=2, label='Model')

pylab.plot(template, color='green', linewidth=2, label='Template')

pylab.legend()

pylab.savefig('dope_profile.png', dpi=65)

The error is :

File "plot_profiles.py", line 14

for n, res in enumerate (seq.residues):

SyntaxError: invalid syntax

Please let me know how i can rectify the script.

Many thanks,

Munishika Kalia