---------- 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. > > -----Inline Attachment Follows----- > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >