Difference between revisions of "CD task4 protocol"

From Bioinformatikpedia
(Alignment)
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# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## o$
 
# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## o$
 
aln = alignment(env)
 
aln = alignment(env)
mdl = model(env, file='2GU2', model_segment=('FIRST:@', 'END:'))
+
mdl = model(env, file='2GU2', model_segment=('FIRST:A', 'END:A'))
 
aln.append_model(mdl, align_codes='2GU2', atom_files='2GU2')
 
aln.append_model(mdl, align_codes='2GU2', atom_files='2GU2')
 
aln.append(file='../p45381.pir', align_codes='p45381')
 
aln.append(file='../p45381.pir', align_codes='p45381')
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aln.write(file='aspa_2gu2.ali', alignment_format='PIR')
 
aln.write(file='aspa_2gu2.ali', alignment_format='PIR')
   
  +
==Single template modelling==
==Default settings==
 

Revision as of 15:45, 29 May 2012

Modeller

We modified the scripts provided in the tutorial to suit our demands.

Target

The sequence of out target Aspartoacylase saved in .pir format:

>P1;p45381
sequence:p45381:::::::0.00: 0.00
MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
LTLNAKSIRCCLH


Alignment

Example alignment script for creating the pairwise alignment of 2GU2 and Aspa.

from modeller import *
env = environ()
# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## o$
aln = alignment(env)
mdl = model(env, file='2GU2', model_segment=('FIRST:A', 'END:A'))
aln.append_model(mdl, align_codes='2GU2', atom_files='2GU2')
aln.append(file='../p45381.pir', align_codes='p45381')
aln.align2d()
aln.check()
aln.write(file='aspa_2gu2-2d.ali', alignment_format='PIR')
aln.malign()
aln.check()
aln.write(file='aspa_2gu2.ali', alignment_format='PIR')

Single template modelling