Difference between revisions of "Lab Journal - Task 5 (PAH)"
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(→Modeller) |
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An example python script for template: 1j8u: |
An example python script for template: 1j8u: |
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| + | <source py> |
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| − | from modeller import * |
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| + | from modeller import * |
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| − | env = environ() |
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| − | + | env = environ() |
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| + | aln = alignment(env) |
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| − | mdl = model(env, file='1j8u.pdb', model_segment=('FIRST:@', 'END:')) |
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| + | mdl = model(env, file='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_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.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.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.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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| + | 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() |
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| + | </source> |
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=== Swissmodel === |
=== Swissmodel === |
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Revision as of 13:31, 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 script for template: 1j8u: <source py> 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() </source>
