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

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

Revision as of 14:17, 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: 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