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"> |
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| − | <code> |
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| + | {| |
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| − | from modeller import * |
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| + | |<code> |
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| − | env = environ() |
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| + | |from modeller import * |
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| − | aln = alignment(env) |
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| + | |env = environ() |
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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 = alignment(env) |
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| − | aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u') |
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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(file='target.pir', align_codes='2pah') |
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| + | |aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u') |
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| − | aln.align2d() |
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| + | |aln.append(file='target.pir', align_codes='2pah') |
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| − | aln.check() |
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| + | |aln.align2d() |
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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. |
+ | |aln.check() |
| + | |aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah-2d.ali', alignment_format='PIR') |
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| − | aln.check() |
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| + | |aln.malign() |
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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.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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| + | |</code> |
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| − | from modeller.automodel import * |
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| + | |- |
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| − | log.verbose() |
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| + | |<code> |
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| − | env = environ() |
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| + | |from modeller import * |
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| − | a = automodel(env, |
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| + | |from modeller.automodel import * |
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| − | alnfile = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', |
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| + | |log.verbose() |
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| − | knowns = '1j8u', |
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| + | |env = environ() |
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| − | sequence = '2pah', |
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| + | |a = automodel(env, |
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| − | assess_methods=(assess.DOPE, assess.GA341)) |
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| + | | alnfile = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', |
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| − | a.starting_model= 1 |
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| − | + | | knowns = '1j8u', |
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| + | | sequence = '2pah', |
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| − | a.make() |
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| + | | assess_methods=(assess.DOPE, assess.GA341)) |
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| − | </code> |
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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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| + | |</code> |
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| + | |} |
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=== Swissmodel === |
=== Swissmodel === |
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Revision as of 13:19, 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">
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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') | |
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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() |
