Greetings , After went through the Basic tutorial , I wanted to build a model from multiple templates (as shown at http://www.salilab.org/modeller/manual/node21.html) For that it says "-- simply provide an alignment between all of the templates and..." So to create the alignment between all of the templates,I modified the script "align2d.py" of step 3 (Aligning TvLDF with the template) in Basic tutorial , as follows: ------------------------------------------------------------- from modeller import * env = environ() aln = alignment(env) #modified from here to add several templates #template 1 mdl = model(env, file='1bdm', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='1bdmA', atom_files='1bdm.pdb') #template 2 mdl = model(env, file='1b8p', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='1b8pA', atom_files='1b8p.pdb') #template 3... #template 4... aln.append(file='TvLDH.ali', align_codes='TvLDH') aln.align2d() aln.write(file='TvLDH-mult.ali', alignment_format='PIR') aln.write(file='TvLDH-mult.pap', alignment_format='PAP') ------------------------------------------------------------- Then using the generated "TvLDH-mult.ali" file I am going to do the automdelling with multiple templates. Is this process correct? Thanks in advance. Umanga