[Biopython] SVDSuperimposer()

[João Rodrigues]

Hi George,

Sorry for the delay in the answer..

Are you doing the minimization using Biopython? That's the only way I see
in which the SVDSuperimposer is a bottleneck. In any case, the SVD code is
written in C, so it should be pretty fast. Can you identify precisely where
the bottleneck is (atom selection, fitting, calculation, etc)?

Anyway, I would suggest looking into some weak position restraints on the
heavy atoms of the backbone to keep things sort of in place. This would
avoid the RMSD calculations at every step (I guess?), instead just a simple
harmonic potential calculation added to the energy function.

Cheers,

João




2014-04-11 18:22 GMT+02:00 George Devaniranjan <devaniranjan at gmail.com>:

> 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
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>
>>
>>
>