[Chimera-users] drawing elipsolids
tef at cgl.ucsf.edu
Wed Dec 2 18:54:05 PST 2009
I've recently spoken to Conrad and Eric about incorporating ellipsoid
trajectories into Chimera in order to support a request from Matt
Jacobson. Perhaps more general support for ellipsoids should be
discussed at tomorrow's Chimera's developers meeting.
Thomas Goddard wrote:
> Hi Keren,
> The BioVEC paper uses quaternions to orient the ellipsoids. If I
> made the Chimera "shape" command able to orient with quaternions (maybe
> rotation axis and angle too) and specify a center and lengths of major
> axes would that be useful?
> For coarse grain models you probably have many ellipsoids and using
> the Chimera command language and shape command may not be the way to go.
> If the ellipsoids are specified in a file, may you really need some
> Python code to import that file and produce all the ellipsoids.
> Also if you want to draw links between the ellipsoids then we should
> think about how to solve the more complex problem. You could make links
> just be cylinders with the "shape" command. But going this route just
> gets you a graphical object with ellipsoids and cylinders and Chimera
> has no idea that the objects are connected. This will limit what you
> can do with such a model. So if you will need Chimera to understand
> structure hierarchy with ellipsoid nodes then we should discuss further
> (could meet tomorrow).
>> Tom - this is a relevant paper for the ellipsoid visualization. Keren
>> Abrahamsson and Plotkin. BioVEC: a program for biomolecule visualization
>> with ellipsoidal coarse-graining. J Mol Graph Model (2009) vol. 28 (2)
>> pp. 140-5
> -------- Original Message --------
> Subject: Re: [Chimera-users] drawing elipsolids
> From: Keren Lasker
> To: Thomas Goddard
> Date: 12/2/09 5:32 PM
>> Thanks Tom!
>> It would be quite useful to have the shape command include ellipsoids.
>> As I intend to use it for low resolution visualization purposes, the
>> axes would not necessarily be aligned to the natural coordinate system.
>> Thanks again ! :)
>> On Dec 2, 2009, at 5:09 PM, Thomas Goddard wrote:
>>> Hi Keren,
>>> There is currently no Chimera command to draw a generic ellipsoid.
>>> The natural command to do this would be "shape" which currently can
>>> draw spheres, cylinders, icosahedrons, ... but not ellipsoids.
>>> The "measure inertia" command draws an ellipsoid matching the moment
>>> of inertia of specified atoms or surfaces.
>>> Chimera can also draw thermal ellipsoids from anisotropic B-factors
>>> given in PDB ANISOU records.
>>> Some Python code can of course make ellipsoids.
>>> Let me know if you'd like the shape command enhanced to include
>>> ellipsoids and whether axes not aligned with x,y,z are needed.
>>> -------- Original Message --------
>>> Subject: [Chimera-users] drawing elipsolids
>>> From: Keren Lasker
>>> To: chimera-users
>>> Date: 12/2/09 3:36 PM
>>>> Dear Chimera team,
>>>> Is there a way to draw ellipsoids in Chimera. The ellipsoid is
>>>> defined by its center and 3 radii.
>>>> Thanks for your help.
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