Difference between revisions of "CD task4 protocol"

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(Modeller)
(Alignments for different templates)
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==Alignments for different templates==
 
==Alignments for different templates==
   
  +
<figtable>
 
 
<table>
 
<table>
 
<tr>
 
<tr>
 
<td>2GU2</td>
 
<td>2GU2</td>
<td><figure>[[File:modeller_2gu2_align.png]]</figure></td>
+
<td><figure id="2gu2_align">[[File:modeller_2gu2_align.png]]</figure></td>
 
</tr>
 
</tr>
   
 
<tr>
 
<tr>
 
<td>3NFZ</td>
 
<td>3NFZ</td>
<td><figure>[[File:modeller_3nfz_align.png]]</figure></td>
+
<td><figure id="3nfz_align">[[File:modeller_3nfz_align.png]]</figure></td>
 
</tr>
 
</tr>
   
 
</table>
 
</table>
</figtable>
 

Revision as of 13:38, 30 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

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">Modeller 2gu2 align.png</figure>
3NFZ <figure id="3nfz_align">Modeller 3nfz align.png</figure>