[Chimera-users] drawing ellipsolids
kerenl at salilab.org
Wed Dec 2 18:03:49 PST 2009
Tom thanks. For my current purposes a simple shape command that can
visualize ellipsoids would do :) Keren.
On Dec 2, 2009, at 5:50 PM, 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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