hi,
Lets say I have two proteins A and B and I want to calculate a distance restraint between them. Usually it would be preferable to calculate the distance restraint between their centroids. However, their centroids are derived from the positions of their atoms. So - even if I calculate the centroids of the protein particle and add XYZ attributes, the calculating of the distance restraint will be true for the first time - but the state of the XYZ attributes of the protein particles should be updated according to the atom positions.
Has anyway come across this issue before?
thanks, Keren.
Keren Lasker wrote: > hi, > > Lets say I have two proteins A and B and I want to calculate a > distance restraint between them. > Usually it would be preferable to calculate the distance restraint > between their centroids. > However, their centroids are derived from the positions of their atoms. > So - even if I calculate the centroids of the protein particle and add > XYZ attributes, the calculating of the distance restraint will be true > for the first time - but the state of the XYZ attributes of the > protein particles should be updated according to the atom positions. > > Has anyway come across this issue before?
There is an example doing more or less this with covering the points with spheres instead of centroids, but the idea is the same.
Keren Lasker wrote: > Lets say I have two proteins A and B and I want to calculate a distance > restraint between them. > Usually it would be preferable to calculate the distance restraint > between their centroids. > However, their centroids are derived from the positions of their atoms. > So - even if I calculate the centroids of the protein particle and add > XYZ attributes, the calculating of the distance restraint will be true > for the first time - but the state of the XYZ attributes of the protein > particles should be updated according to the atom positions.
One option is to use a GravityCenterScoreState to keep each gravity center particle at the center of mass of its parent particles.
Ben
thanks Ben ! but do you mean to keep each gravity > > center particle at the center of mass of its CHILDREN particles. ? On Jan 26, 2009, at 7:46 AM, Ben Webb wrote:
> Keren Lasker wrote: >> Lets say I have two proteins A and B and I want to calculate a >> distance >> restraint between them. >> Usually it would be preferable to calculate the distance restraint >> between their centroids. >> However, their centroids are derived from the positions of their >> atoms. >> So - even if I calculate the centroids of the protein particle and >> add >> XYZ attributes, the calculating of the distance restraint will be >> true >> for the first time - but the state of the XYZ attributes of the >> protein >> particles should be updated according to the atom positions. > > One option is to use a GravityCenterScoreState to keep each gravity > center particle at the center of mass of its parent particles. > > 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
Keren Lasker wrote: > but do you mean to keep each gravity > center particle at the center of mass of its CHILDREN particles. > ?
The gravity center ScoreState simply keeps a list of particles and positions itself at the center of gravity of those particles. Whether you think of the particles in that list as children or parents is a matter of your viewpoint, I suppose.
Ben
On Jan 26, 2009, at 10:09 AM, Ben Webb wrote:
> Keren Lasker wrote: >> but do you mean to keep each gravity >> center particle at the center of mass of its CHILDREN particles. >> ? > > The gravity center ScoreState simply keeps a list of particles and > positions itself at the center of gravity of those particles. Whether > you think of the particles in that list as children or parents is a > matter of your viewpoint, I suppose. I think I had only replied to Keren before. There is an example which does more or less what she wanted to do (in simple examples).
participants (3)
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Ben Webb -
Daniel Russel -
Keren Lasker