Difference between revisions of "Workflow homology modelling glucocerebrosidase"
From Bioinformatikpedia
(Created page with "== 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-fi…") |
(→Preparation of the Alignment File) |
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# Save PDB-file of template sequence: template:pdb |
# Save PDB-file of template sequence: template:pdb |
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#: If PDB-file consists of several chains: split pdb file with the help of [http://structure.usc.edu/splitpdb/ splitpdb] (note that minor changes are needed, so that the ATOM coordinates are listed in the resulting PDB-file instead of HETATOMS). |
#: If PDB-file consists of several chains: split pdb file with the help of [http://structure.usc.edu/splitpdb/ splitpdb] (note that minor changes are needed, so that the ATOM coordinates are listed in the resulting PDB-file instead of HETATOMS). |
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| − | # Run Python |
+ | # Run the following Python script with command '<code>mod9.9 align.py</code>' to create target template alignment in PIR-format: |
| − | + | <code> |
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log.verbose()<br/> |
log.verbose()<br/> |
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env = environ()<br/> |
env = environ()<br/> |
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aln.write(file='target_template.ali', alignment_format='PIR')<br/> |
aln.write(file='target_template.ali', alignment_format='PIR')<br/> |
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aln.write(file='target_template.pap', alignment_format='PAP')</code> |
aln.write(file='target_template.pap', alignment_format='PAP')</code> |
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| + | |||
| + | === Modeling of the Structure === |
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| + | # Run the following Python script with command '<code>mod9.9 model.py</code>' to model the structure of the target sequence: |
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| + | <code> |
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| + | |||
| + | </code> |
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Revision as of 08:51, 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')
Modeling of the Structure
- Run the following Python script with command '
mod9.9 model.py' to model the structure of the target sequence:
