Workflow homology modelling glucocerebrosidase

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MODELLER

Preparation of the Alignment File

  1. Save target protein sequence in PIR-format: target.pir
  2. 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).
  3. 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')