below On Jan 26, 2010, at 2:29 AM, Daniel Russel wrote:
> > 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. yes - jeremy and i are finalizing something like that for the review, so we should be able to add it soon. > > 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. i had the pleasure of meeting then when working on domino, so - it might be useful for "advanced" usages. > >> 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 > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev