[Chimera-users] drawing ellipsolids

Keren Lasker 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
>> 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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