Difference between revisions of "CD task4 protocol"

From Bioinformatikpedia
(Modeller)
(Alignment)
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==Alignment==
 
==Alignment==
   
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Example alignment script for creating the pairwise alignment of 2GU2 and Aspa.
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  +
from modeller import *
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env = environ()
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# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## o$
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aln = alignment(env)
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mdl = model(env, file='2GU2', model_segment=('FIRST:@', 'END:'))
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aln.append_model(mdl, align_codes='2GU2', atom_files='2GU2')
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aln.append(file='../p45381.pir', align_codes='p45381')
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aln.align2d()
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aln.check()
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aln.write(file='aspa_2gu2-2d.ali', alignment_format='PIR')
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aln.malign()
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aln.check()
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aln.write(file='aspa_2gu2.ali', alignment_format='PIR')
   
 
==Default settings==
 
==Default settings==

Revision as of 15:30, 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:@', 'END:'))
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')

Default settings