Difference between revisions of "CD task4 protocol"
From Bioinformatikpedia
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==Alignments for different templates== |
==Alignments for different templates== |
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<table> |
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<td>2GU2</td> |
<td>2GU2</td> |
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| − | <td><figure>[[File:modeller_2gu2_align.png]]</figure></td> |
+ | <td><figure id="2gu2_align">[[File:modeller_2gu2_align.png]]</figure></td> |
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<tr> |
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<td>3NFZ</td> |
<td>3NFZ</td> |
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| − | <td><figure>[[File:modeller_3nfz_align.png]]</figure></td> |
+ | <td><figure id="3nfz_align">[[File:modeller_3nfz_align.png]]</figure></td> |
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</table> |
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Revision as of 13:38, 30 May 2012
Contents
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
Example alignment script for creating a model of Aspartoacylase from a single template 2GU2:A.
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ()
# env.io.atom_files_directory = ["/apps/modeller9.9/bin/examples/commands/", "/path/to/your/files/"] ## only needed in the VirtualBox
a = automodel(env,
alnfile = 'aspa_2gu2-2d.ali',
knowns = '2GU2A',
sequence = 'p45381',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1
a.ending_model = 1
a.make()
Alignments for different templates
| 2GU2 | <figure id="2gu2_align"> </figure> |
| 3NFZ | <figure id="3nfz_align"> </figure> |
