[Chimera-users] drawing ellipsolids

Thomas Goddard goddard at cgl.ucsf.edu
Thu Dec 3 17:44:06 PST 2009

Hi Keren,

   I've added command "shape ellipsoid", available in tonight's Chimera 
1.5 daily builds (not in Chimera 1.4).  The command would look like

	shape ellipsoid radius 1.5,2.8,4.5 rotation 1,0,0,45

where the radii are specified along the x,y,z axes, and a rotation by 45 
degrees about the x axis is then applied.  The rotation can be specified 
with quaternions with the qrotation argument.  Keywords can be 
abbreviated.  Updated documentation will appear tomorrow on the web


and will be included with tonight's Chimera 1.5 (view it with Chimera 
command "help shape").


-------- Original Message --------
Subject: Re: [Chimera-users] drawing ellipsolids
From: Keren Lasker
To: Thomas Goddard
Date: 12/2/09 6:03 PM

> 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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