[Biopython] SVDSuperimposer()

[George Devaniranjan]

Hi João,

Ok this is what I do, I use a conjugate gradient minimizer that adjusts the
phi and psi angles of the residues to move the residues around. Of course
small changes in these angles can result in large displacements further
down the chain. I know that the "bad" structure I start with is "close" to
what is expected so as I continue to minimize (using the minimizer in
cycles) I use the RMSD difference as a test to ensure that the "better"
structure while energetically better than the starting one doesn't
look totally different from where I started.

I will look at profit, I have never tried that-thank you very much for the
suggestion.

George


On Fri, Apr 11, 2014 at 12:11 PM, João Rodrigues <anaryin at gmail.com> wrote:

> Hey George,
>
> What do you mean by bottleneck? In terms of speed?
>
> You can always use Profit for example to calculate RMSDs between the
> models. It's a bit faster than our module.
>
> Cheers,
>
> João
>
>
> 2014-04-11 17:58 GMT+02:00 George Devaniranjan <devaniranjan at gmail.com>:
>
>> I was wondering if there is a faster way to do the following.
>>
>>
>> I am minimizing a protein structure and one of the 'measurements" is that
>> the minimized structure be as close to the starting value as possible.
>>
>>
>> Currently I use SVDSuperimposer.SVDSuperimposer() to calculate the RMSD
>> difference.
>>
>>
>> When I checked the various "energy terms" that are used to evaluate the
>> structure I find that the bottleneck is
>> indeed SVDSuperimposer.SVDSuperimposer().
>>
>>
>> Is there a way to do this more efficiently ?
>>
>>
>> Thank you
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>
>