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

From Bioinformatikpedia
(Modeller)
(Modeller)
Line 19: Line 19:
 
<figtable id="mod_pyt">
 
<figtable id="mod_pyt">
 
{|
 
{|
|<code>
 
 
|from modeller import *
 
|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')
|</code>
 
 
|-
 
|-
|<code>
 
 
|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()
|</code>
 
 
|}
 
|}
   

Revision as of 14:20, 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