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?

James

2014-04-15 23:03 GMT+04:00 Modeller Caretaker <modeller-care@salilab.org>:

On 4/15/14, 2:05 AM, James Starlight wrote:

I've followed 1st modeller tutorial making alignment of my target
against 1 template (with the inclusion of hetatm from the template). As
the result I've obtained the below alignment

As pointed out already, you haven't told Modeller to put the ligand in the model. Is it possible that you modified the 2rh1.pdb file? Your template sequence doesn't match the one in 2rh1 from PDB (there's an extra sequence in the official PDB from residue 1002:A to 1161:A that isn't in yours). Maybe you removed the ligand by mistake too.

Ben Webb, Modeller Caretaker
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