You remove the chain identifier from both align2d.py and model_multiple.py (Or, whatever you are using) This is how i did it in one of the run.

Thus, Align2d.py becomes mdl = model(env, file='Run2BestModel',

model_segment=('1','292')) #No ChainID is here with model residue positions aln.append_model(mdl, align_codes='Run2BestModel',

atom_files='Run2BestModel')

So, Model_multiple.py will be a = automodel(env, alnfile = 'alignment.ali', knowns = ('Run2BestModel'), sequence = 'target', assess_methods=(assess.DOPE, assess.GA341,assess.normalized_dope)) a.starting_model= 1 a.ending_model = 1000 a.make()

Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Birla Institute of Technology & Science, Pilani Rajasthan, INDIA