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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

http://salilab.org/modeller/9v7/manual/node247.html
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')
with
    mdl.generate_topology(aln[code+'-ini'])

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