Re: [modeller_usage] model.energy()

[Modeller Caretaker <>]

Jayapal, Prabha wrote:
> I am a new user of MODELLER 9. I got an appreciable model using
> modeller and I would like to evaluate the model by the
> model.energy(). But I got an error like,
...
> transfe_507E> Number of residues in alignment different from that in MODEL:       60      120
>               (Did you call clear_topology() before generate_topology() ?) 
...
> aln = alignment(env)
> code = "nitro.B99990066"
> mdl = model(env, file=code)
> aln.append_model(mdl, atom_files=code, align_codes=code)
> aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini')
>
> mdl.generate_topology(aln[code+'-ini'])

Add the line
mdl.clear_topology()

before the generate_topology() call, if you want to do this the "hard" 
way. Or look at the example at 
http://salilab.org/modeller/9v1/manual/node228.html for an easier way.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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