---------- Forwarded message ----------
From: Krupal Jethava <krupal.jethava@gmail.com>
Date: Mon, Dec 10, 2012 at 6:01 PM
Subject: Re: [modeller_usage] modeling with multiple sequence alignment.
To: flavio seixas <oivalf_nix@yahoo.com>

I have

1) alignment.ali

2) qseq.fasta

2) tseq1.pdb and tseq2.pdb

I tried this script by modeller- "C:\ program files (x86)\ modeller 9.11\ bin \ test> mod9.11 script.py"

# Homology modeling with multiple templates

from modeller import * # Load standard Modeller classes

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

# directories for input atom files

env.io.atom_files_directory = ['.', '../atom_files']

a = automodel(env,

alnfile = 'alignment.ali', # alignment filename

knowns = ('tseq2', 'tseq1'), # codes of the templates

sequence = 'qseq') # code of the target

a.starting_model= 1 # index of the first model

a.ending_model = 1 # index of the last model

# (determines how many models to calculate)

a.make() # do the actual homology modeling

Got these errors

traceback <.......>:

file "script.py", line 18,in ?

a.make()

File ; C:\........\automodel.py, line 424 in homcsr,

File ; C:\........\automodel.py, line 406, in check_alignment

aln.check()

and many.......

What to do?

On Mon, Dec 10, 2012 at 5:22 PM, flavio seixas <oivalf_nix@yahoo.com> wrote:

Hi,

For multiple templates try to follow this example:

http://salilab.org/modeller/9.10/manual/node21.html

Try to put those lines below, at the end of your script model-multiple.py script.
It will display the top five models at the end of your model-multiple.log file.

# Get a list of all successfully built models from a.outputs
ok_models = filter(lambda x: x['failure'] is None, a.outputs)

# Rank the models by DOPE score
key = 'DOPE score'
ok_models.sort(lambda a,b: cmp(a[key], b[key]))

# Get top model
m = ok_models[0]

print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[1]

print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[2]

print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[3]

print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key])
m =
ok_models[4]

print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key])

Regards,

Flavio

--- On Mon, 12/10/12, Krupal Jethava <krupal.jethava@gmail.com> wrote:

From: Krupal Jethava <krupal.jethava@gmail.com>
Subject: [modeller_usage] modeling with multiple sequence alignment.
To: modeller_usage@salilab.org
Date: Monday, December 10, 2012, 11:26 AM

Dear Sir, I am trying to use modeller for multiple sequence alignment but I got error while running script for DOPE score. will you guide from the beginning. how to make input file and which script should I use for that. Thanks.

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