currently, we do not have too many particles. but of course it'd be nice to have a faster restraint in any case ;)

tx

frido

On Wed, Dec 3, 2008 at 8:01 PM, Daniel Russel <drussel@gmail.com> wrote:
Keren Lasker wrote:
> Ben - I might be missing something here but the centroid changes at
> each optimization step - so this means that the particle will converge
> slower in the O(N) suggestion than in the O(N^2) suggestion - since
> the centroid of the previous iteration will hold it back.
>
The score state is updated before the restraints are evaluated, so it
will always have the position of the current centroid.

> On Dec 3, 2008, at 7:36 PM, Ben Webb wrote:
>
>
>> Friedrich Foerster wrote:
>>
>>> for the 26s project i would like to use a maximum diameter restraint
>>> on the shape of proteins. so it'd be a restraint similar to the
>>> connectivity restraint: all distances in a protein are evaluated and
>>> if the largest distance is above a specified threshold, a harmonic
>>> restraint would be applied on the respective pair.
>>>
>> The solution already proposed by Daniel looks perfect to me as a
>> literal
>> solution to your problem, but is that really what you want to do:
>> constrain every particle pair in the protein to less than the
>> diameter?
>> If you have a lot of particles, that's going to become expensive
>> rather
>> quickly (O(N^2), obviously). Another option to consider would be to
>> constrain every particle to be less than the radius from the protein
>> center. That would give you far fewer restraints and scale as O(N).
>> You
>> could do this with a bunch of DistanceToSingletonScores if the protein
>> center is at a fixed point, or use a GravityCenterScoreState to
>> stick a
>> particle at the center of gravity of your protein, and then use
>> regular
>> distance restraints between each particle and that center.
>>
>>      Ben
>> --
>> ben@salilab.org                      http://salilab.org/~ben/
>> "It is a capital mistake to theorize before one has data."
>>      - Sir Arthur Conan Doyle
>> _______________________________________________
>> IMP-dev mailing list
>> IMP-dev@salilab.org
>> https://salilab.org/mailman/listinfo/imp-dev
>>
>
> _______________________________________________
> IMP-dev mailing list
> IMP-dev@salilab.org
> https://salilab.org/mailman/listinfo/imp-dev
>

_______________________________________________
IMP-dev mailing list
IMP-dev@salilab.org
https://salilab.org/mailman/listinfo/imp-dev