Re: [modeller_usage] Regarding energy minimization in modeller

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
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