Difference between revisions of "Lab Journal - Task 5 (PAH)"
From Bioinformatikpedia
(→Modeller) |
(→Modeller) |
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An example python call for template: 1j8u: |
An example python call for template: 1j8u: |
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| + | from modeller import * |
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| − | <figtable id="mod_pyt"> |
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| − | |||
| − | <code>from modeller import * |
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env = environ() |
env = environ() |
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aln = alignment(env) |
aln = alignment(env) |
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| − | mdl = model(env, file=' |
+ | mdl = model(env, file='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') |
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aln.append(file='target.pir', align_codes='2pah') |
aln.append(file='target.pir', align_codes='2pah') |
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Revision as of 13:24, 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='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()
