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Re: [modeller_usage] Regarding energy minimization in modeller

On 07/27/2009 09:32 AM, snoze pa wrote:
  I am using modeller to build some homology model. But I am unable to
find any script that can be used to minimize the structure. Is there
any script available in modeller that can be used to energy minimize
the modeled structure.

There is no need to perform any kind of energy minimization on the structure, because that's already been done - that's what Modeller does when it builds a homology model (constructs a scoring function from the available data, then minimizes it). But if you really want to minimize using some other scoring function (set of restraints) then you could write a script similar to that at
Of course, you will have to decide what set of restraints to use.

I try to use the old script, model_energies.py
but it give me following error message

Traceback (most recent call last):
  File "model_energies.py", line 41, in ?
    mdl.generate_topology(aln, sequence=code+'-ini')
TypeError: generate_topology() got an unexpected keyword argument 'sequence'

I don't know what script you are referring to here, but to fix that Python error you can replace
    mdl.generate_topology(aln, sequence=code+'-ini')

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage