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

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(Modeller)
(Modeller)
Line 17: Line 17:
   
 
An example python call for template: 1j8u:
 
An example python call for template: 1j8u:
  +
<figtable id="mod_pyt">
<code>
 
  +
{|
from modeller import *
 
  +
|<code>
env = environ()
 
  +
|from modeller import *
aln = alignment(env)
 
  +
|env = environ()
mdl = model(env, file='/mnt/home/student/waldraffs/masterpracitcal/Task5/1j8u.pdb', model_segment=('FIRST:@', 'END:'))
 
  +
|aln = alignment(env)
aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u')
 
  +
|mdl = model(env, file='/mnt/home/student/waldraffs/masterpracitcal/Task5/1j8u.pdb', model_segment=('FIRST:@', 'END:'))
aln.append(file='target.pir', align_codes='2pah')
 
  +
|aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u')
aln.align2d()
 
  +
|aln.append(file='target.pir', align_codes='2pah')
aln.check()
 
  +
|aln.align2d()
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-2d.ali', alignment_format='PIR')
aln.check()
 
  +
|aln.malign()
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', alignment_format='PIR')
 
  +
|aln.check()
 
  +
|aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', alignment_format='PIR')
from modeller import *
 
  +
|</code>
from modeller.automodel import *
 
  +
|-
log.verbose()
 
  +
|<code>
env = environ()
 
  +
|from modeller import *
a = automodel(env,
 
  +
|from modeller.automodel import *
alnfile = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali',
 
  +
|log.verbose()
knowns = '1j8u',
 
  +
|env = environ()
sequence = '2pah',
 
  +
|a = automodel(env,
assess_methods=(assess.DOPE, assess.GA341))
 
  +
| alnfile = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali',
a.starting_model= 1
 
a.ending_model = 1
+
| knowns = '1j8u',
  +
| sequence = '2pah',
a.make()
 
  +
| assess_methods=(assess.DOPE, assess.GA341))
</code>
 
  +
|a.starting_model= 1
  +
|a.ending_model = 1
  +
|a.make()
  +
|</code>
  +
|}
   
 
=== Swissmodel ===
 
=== Swissmodel ===

Revision as of 14:19, 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