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.
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.htm... 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.
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.htm...
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.
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&_us... <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-4W9XF04-1&_us...>
-------- 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.htm...
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.
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&_us... <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-4W9XF04-1&_us...
-------- 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.htm...
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.
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 http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html and will be included with tonight's Chimera 1.5 (view it with Chimera command "help shape"). Tom -------- 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&_us... <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-4W9XF04-1&_us...>
-------- 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.htm...
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.
Tom, 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. --tom 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&_us... <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGP-4W9XF04-1&_us...>
-------- 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.htm...
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.
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Keren Lasker -
Thomas Goddard -
Tom Ferrin