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$ |
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aln = alignment(env) |
aln = alignment(env) |
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| − | mdl = model(env, file='2GU2', model_segment=('FIRST: |
+ | 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') |
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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') |
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| + | ==Single template modelling== |
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| − | ==Default settings== |
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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')
