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.
>>>>
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