I have been modelling GPCRs using multiple templates and have noticed that in the code below in my salign.py file:
aln = alignment(env)
for (code, chain) in (('1', 'A'), ('2', 'A'), ('3', 'A')):
mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain))
aln.append_model(mdl, atom_files=code, align_codes=code+chain)
if I switched the order of the templates to be 3, 1, 2 instead of the order shown above (1,2,3), I get different models with different DOPE scores. Is this possible or am I doing something wrong? If this is the case, how can I determine which order of my templates is optimal for homology modelling? Thanks in advance,
HIDDEN