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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >