[Chimera-users] drawing elipsolids

Thomas Goddard goddard at cgl.ucsf.edu
Wed Dec 2 17:50:14 PST 2009

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
> 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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