Workflow homology modelling glucocerebrosidase
From Bioinformatikpedia
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 Python Script with command '
mod9.9 align.py
' to align the two sequences:
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')