Difference between revisions of "Workflow homology modelling glucocerebrosidase"
From Bioinformatikpedia
(→MODELLER) |
(→Modelling of the Target Structure) |
||
| Line 20: | Line 20: | ||
# Run the following Python script with command '<code>mod9.9 model.py</code>' to model the structure of the target sequence: |
# Run the following Python script with command '<code>mod9.9 model.py</code>' to model the structure of the target sequence: |
||
<code> |
<code> |
||
| − | from modeller.automodel import * |
+ | from modeller.automodel import * <br/> |
| − | log.verbose() |
+ | log.verbose()<br/> |
| − | env = environ() |
+ | env = environ()<br/> |
| + | env.io.atom_files_directory = ''<br/> |
||
| − | |||
| + | a = automodel (env, alnfile = '1OGS_2NT0.ali', knowns = '2NT0', sequence = '1OGS')<br/> |
||
| − | env.io.atom_files_directory = '' |
||
| + | a.starting_model = 1<br/> |
||
| − | a = automodel (env, |
||
| + | a.ending_model = 1<br/> |
||
| − | alnfile = '1OGS_2NT0.ali', |
||
| + | a.make()<br/> |
||
| − | knowns = '2NT0', |
||
| − | sequence = '1OGS') |
||
| − | a.starting_model = 1 |
||
| − | a.ending_model = 1 |
||
| − | a.make() |
||
</code> |
</code> |
||
Revision as of 08:52, 10 June 2011
MODELLER
Preparation of the Alignment File
- Save target protein sequence in PIR-format: target.pir
- Save PDB-file of template sequence: template:pdb
- If PDB-file consists of several chains: split pdb file with the help of splitpdb (note that minor changes are needed, so that the ATOM coordinates are listed in the resulting PDB-file instead of HETATOMS).
- Run the following Python script with command '
mod9.9 align.py' to create target template alignment in PIR-format:
log.verbose()
env = environ()
aln = alignment(env)
mdl= model(env, file='template')
aln.append_model(mdl, align_codes='template')
aln.append(file='target.pir', align_codes=('target'))
aln.align(gap_penalties_1d=(-600,-400))
aln.write(file='target_template.ali', alignment_format='PIR')
aln.write(file='target_template.pap', alignment_format='PAP')
Modelling of the Target Structure
- Run the following Python script with command '
mod9.9 model.py' to model the structure of the target sequence:
from modeller.automodel import *
log.verbose()
env = environ()
env.io.atom_files_directory =
a = automodel (env, alnfile = '1OGS_2NT0.ali', knowns = '2NT0', sequence = '1OGS')
a.starting_model = 1
a.ending_model = 1
a.make()
