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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<figtable id="mod_pyt"> |
<figtable id="mod_pyt"> |
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| + | |||
| − | {| |
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| − | + | <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') |
| + | |||
| − | |- |
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| − | + | 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', |
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knowns = '1j8u', |
knowns = '1j8u', |
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sequence = '2pah', |
sequence = '2pah', |
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assess_methods=(assess.DOPE, assess.GA341)) |
assess_methods=(assess.DOPE, assess.GA341)) |
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| − | a.starting_model= 1 |
+ | a.starting_model= 1 |
| − | a.ending_model = 1 |
+ | a.ending_model = 1 |
| − | a.make() |
+ | a.make() |
| + | |||
| − | |} |
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=== Swissmodel === |
=== Swissmodel === |
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Revision as of 13:22, 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
