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[modeller_usage] Fwd: modeling with multiple sequence alignment.



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


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 <" target="_blank">> 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 <" target="_blank">> wrote:

From: Krupal Jethava <" target="_blank">>
Subject: [modeller_usage] modeling with multiple sequence alignment.
To: " target="_blank">
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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