Thanks for suggestions again!
Could you tell me as well
1) what should I provide to the below ali.py script to copy HETATM from the template to the model
env = environ()
aln = alignment(env)
# Read in HETATM records from template PDBs
env.io.hetatm = True
env.io.hydrogen= True
mdl = model(env, file='3eml', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='3emlA', atom_files='3eml.pdb')
aln.append(file='od_r.ali', align_codes='od_r')
aln.align2d()
aln.write(file='result3.ali', alignment_format='PIR')
aln.write(file='result3.pap', alignment_format='PAP')
2) how salt bridges can be defined in the model taken from the template with the homology
cysteins in the same positions?