[Chimera-users] drawing elipsolids

Tom Ferrin 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
>> 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
>> http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-4W9XF04-1&_user=4430&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000059594&_version=1&_urlVersion=0&_userid=4430&md5=1ba4c2e8837d10be57c86710dc862989 
>> <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-4W9XF04-1&_user=4430&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000059594&_version=1&_urlVersion=0&_userid=4430&md5=1ba4c2e8837d10be57c86710dc862989>
> -------- 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 ! :)
>> Keren.
>> 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.
>>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html
>>> The "measure inertia" command draws an ellipsoid matching the moment 
>>> of inertia of specified atoms or surfaces.
>>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia 
>>> Chimera can also draw thermal ellipsoids from anisotropic B-factors 
>>> given in PDB ANISOU records.
>>> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html 
>>> 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.
>>>     Tom
>>> -------- 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.
>>>> Best,
>>>> Keren.
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