Difference between revisions of "Lab Journal - Task 5 (PAH)"

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(Modeller)
(Modeller)
Line 18: Line 18:
 
An example python call for template: 1j8u:
 
An example python call for template: 1j8u:
 
<figtable id="mod_pyt">
 
<figtable id="mod_pyt">
  +
{|
 
|from modeller import *
+
<code>from modeller import *
env = environ()
+
env = environ()
aln = alignment(env)
+
aln = alignment(env)
mdl = model(env, file='/mnt/home/student/waldraffs/masterpracitcal/Task5/1j8u.pdb', model_segment=('FIRST:@', 'END:'))
+
mdl = model(env, file='/mnt/home/student/waldraffs/masterpracitcal/Task5/1j8u.pdb', model_segment=('FIRST:@', 'END:'))
aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u')
+
aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u')
aln.append(file='target.pir', align_codes='2pah')
+
aln.append(file='target.pir', align_codes='2pah')
aln.align2d()
+
aln.align2d()
aln.check()
+
aln.check()
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah-2d.ali', alignment_format='PIR')
+
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah-2d.ali', alignment_format='PIR')
aln.malign()
+
aln.malign()
aln.check()
+
aln.check()
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', alignment_format='PIR')
+
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', alignment_format='PIR')
  +
|-
 
|from modeller import *
+
from modeller import *
from modeller.automodel import *
+
from modeller.automodel import *
log.verbose()
+
log.verbose()
env = environ()
+
env = environ()
a = automodel(env,
+
a = automodel(env,
 
alnfile = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali',
 
alnfile = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali',
 
knowns = '1j8u',
 
knowns = '1j8u',
 
sequence = '2pah',
 
sequence = '2pah',
 
assess_methods=(assess.DOPE, assess.GA341))
 
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1
+
a.starting_model= 1
a.ending_model = 1
+
a.ending_model = 1
a.make()
+
a.make()
  +
|}
 
   
 
=== Swissmodel ===
 
=== Swissmodel ===

Revision as of 14:22, 5 June 2013

Model calculation

Modeller

To use Modeller we follow the tutorial written by the students 2011.

  • First the target sequence must be provided into PIR-format (2pah has one Lysine at the end and therefore is one aa longer than P00439???):

>P1;2pah
sequence:2pah:::::::0.00: 0.00
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV
NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM
EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF
RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE
KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR
IEVLDNTQQLKILADSINSEIGILCSALQKIK*

An example python call for template: 1j8u: <figtable id="mod_pyt">

from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='/mnt/home/student/waldraffs/masterpracitcal/Task5/1j8u.pdb', model_segment=('FIRST:@', 'END:'))
aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u')
aln.append(file='target.pir', align_codes='2pah')
aln.align2d()
aln.check()
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah-2d.ali', alignment_format='PIR') 
aln.malign()
aln.check()
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', alignment_format='PIR')
from modeller import *
from modeller.automodel import *    
log.verbose()   
env = environ() 
a = automodel(env,
            alnfile  = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali',   
            knowns   = '1j8u',              
            sequence = '2pah',
            assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1                
a.ending_model  = 1                
a.make()


Swissmodel

iTasser

Model evaluation