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