On Jan 25, 2010, at 4:01 PM, Keren Lasker wrote:
> yes - this looks good, as long as it follows with examples for protein rigid bodies, usage of that in optimization, A protein example would be good. Do you have something simple around from experimenting for multifit? A couple of proteins and simple distance restraints that provide a unique relative orientation for example.
Do we have something we can on discussing rigid body modeling in general with biological structures?
> maybe also something about relevant score-states. No one should ever see them, so definitely not documenting them.
> Also - there is this issue of moving a rigid body that does not really does anything unless a flag is set That is long gone :-)
> - maybe it would be good to explain the mechanism of rigid body movements. Yeah, I'll add a mention of constraints and a link to the constraints page in an advanced section.
> Also - for optimization it might be useful to mention the RigidBodyMover. Indeed, you should have added a link when you wrote it :-) I've added one.
> On Jan 26, 2010, at 1:56 AM, Daniel Russel wrote: > >> Is this a better overview of rigid bodies text? The previous one was not well structured. >> >> A rigid body particle describes a set of particles, known >> as the members, which move rigidly together. Since the >> members are simply a set of particles which move together >> they don't (necessarily) define a shape. For example, >> the members could include representations of the geometry >> at several different representations. As a result, methods >> that use rigid bodies also take a Refiner. This refiner >> is used to map from the rigid body to the set of particles >> defining the geometry of interest. >> >> The initial orientation of the rigid body is computed from >> the coordinates, masses and radii of the particles >> passed to the constructor, based on diagonalizing the >> inertial tensor (which is not stored, currently). >> >> A rigid body stores the a set of local coordinates for each >> member and an algebra::Transformation3D mapping between >> the local coordinates and the actual location of the member. >> >> It is often desirable to randomize the orientation of a rigid >> body: >> \verbinclude randomize_rigid_body.py >> >> >> On Jan 25, 2010, at 3:33 PM, Keren Lasker wrote: >> >>> thanks Daniel. >>> Is there a function for each of those ? if so it would be useful to explicitly have it in the documentation. >>> and specifically for my current requirement - what is the function for getting the set of particles which defines the highest resolution description of the shape, if the rigid body is not defined by atom::Hierarchy. >>> ? >>> On Jan 26, 2010, at 1:27 AM, Daniel Russel wrote: >>> >>>> On Jan 25, 2010, at 3:20 PM, Keren Lasker wrote: >>>> >>>>> To get the particles within a rigid body, it is better using IMP::core::get_leaves or get_members, >>>> Maybe :-) They do different things (that might happen to have the same result sometimes). >>>> >>>> >>>>> i.e.: does get_members return the leaves or the children of the RigidBody ? >>>> neither, it returns all particles which move rigidly with the rigid body. >>>> >>>> Basically, when you have a shape that happens to be rigid, there are many sets of particles associated with it >>>> - all particles which movie rigidly with the shape (the rigid members) >>>> - the set of particles which defines the highest resolution description of the shape (which, if the rigid body is created from a molecular hierarchy, would be the leaves) >>>> - the set of particles which defines the coarsest description of the shape. Typically this is just the rigid body particle itself with a radius >>>> - the set of particles defining the residues in the rigid body >>>> - the particles defining the sphere hierarchy used for collision detection between that rigid hierarchy and another rigid hierarchy (which would be members, if they existed) >>>> etc. >>>> >>>> Depending on what you want to do, you will need different ones of these sets. >>>> >>>> _______________________________________________ >>>> 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 > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev