[Biopython] SVDSuperimposer()

[George Devaniranjan]

Oh, sorry-yes I meant the speed.


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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>
>