Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe
Dear Giuseppe, You can use "Axes/Planes" (under Tools... Structure Analysis) to define an axis object for a selected set of atoms. If "Mass weighting" is on and "Use helical correction" is off, the axis is equivalent to the longest axis of the ellipsoid from "measure inertia." You could also choose not to use mass weighting, whereas the ellipsoid approach always uses mass weighting. Currently, however the axis approach only gives the first principle axis; there is no option to also generate the second and third, as used to define an ellipsoid. Axis and plane objects can also be created with the command "define," for example: define axis helical false mass true color red radius 2 sel to show the mass-weighted principal axis of the currently selected atoms. Axis and plane objects can be used in various distance and angle measurements using the Axes/Planes interface or commands. In version 1.5 of Chimera (daily builds), there are also centroid objects and the tools is named "Axes/Planes/Centroids." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 11, 2010, at 6:23 AM, Giuseppe Falini wrote:
Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe
Thanks giuseppe -----Messaggio originale----- Da: Elaine Meng [mailto:meng@cgl.ucsf.edu] Inviato: giovedì 11 febbraio 2010 20.21 A: Giuseppe Falini Cc: chimera-users@cgl.ucsf.edu Oggetto: Re: [Chimera-users] help Dear Giuseppe, You can use "Axes/Planes" (under Tools... Structure Analysis) to define an axis object for a selected set of atoms. If "Mass weighting" is on and "Use helical correction" is off, the axis is equivalent to the longest axis of the ellipsoid from "measure inertia." You could also choose not to use mass weighting, whereas the ellipsoid approach always uses mass weighting. Currently, however the axis approach only gives the first principle axis; there is no option to also generate the second and third, as used to define an ellipsoid. Axis and plane objects can also be created with the command "define," for example: define axis helical false mass true color red radius 2 sel to show the mass-weighted principal axis of the currently selected atoms. Axis and plane objects can be used in various distance and angle measurements using the Axes/Planes interface or commands. In version 1.5 of Chimera (daily builds), there are also centroid objects and the tools is named "Axes/Planes/Centroids." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 11, 2010, at 6:23 AM, Giuseppe Falini wrote:
Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe
Dear Elaine, I applied your suggestion and all works as you described. The main problem is that I need of the second axis of the ellipsoid, since the comparing subunits mainly rotate along the main axis. I hope that in the future you will develop this option Thanks giuseppe -----Messaggio originale----- Da: Elaine Meng [mailto:meng@cgl.ucsf.edu] Inviato: giovedì 11 febbraio 2010 20.21 A: Giuseppe Falini Cc: chimera-users@cgl.ucsf.edu Oggetto: Re: [Chimera-users] help Dear Giuseppe, You can use "Axes/Planes" (under Tools... Structure Analysis) to define an axis object for a selected set of atoms. If "Mass weighting" is on and "Use helical correction" is off, the axis is equivalent to the longest axis of the ellipsoid from "measure inertia." You could also choose not to use mass weighting, whereas the ellipsoid approach always uses mass weighting. Currently, however the axis approach only gives the first principle axis; there is no option to also generate the second and third, as used to define an ellipsoid. Axis and plane objects can also be created with the command "define," for example: define axis helical false mass true color red radius 2 sel to show the mass-weighted principal axis of the currently selected atoms. Axis and plane objects can be used in various distance and angle measurements using the Axes/Planes interface or commands. In version 1.5 of Chimera (daily builds), there are also centroid objects and the tools is named "Axes/Planes/Centroids." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 11, 2010, at 6:23 AM, Giuseppe Falini wrote:
Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe
Hi Guiseppe, I guess you are using the Chimera "measure inertia" command to show an inertia ellipsoid for specific atoms. There is not an option to show the principal axes as arrows. I'll add that to our feature request list. But you can do it now by hand if it is worth going to that trouble. You would use Chimera BILD format to draw the axes as in the following mailing list message http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003762.html but you would use the axes that the measure inertia command reports in the reply log. Tom
Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe
Hi Giuseppe, I've made the Chimera "measure inertia" command report the center of the ellipsoid in the Reply Log. The output looks like: Inertia axes for 3BQW.pdb v1 = -0.363 -0.271 -0.892 a = 39.714 r1 = 14.386 v2 = 0.853 -0.482 -0.200 b = 26.633 r2 = 19.507 v3 = 0.375 0.833 -0.406 c = 18.039 r3 = 21.385 center = 34.324 8.2127 2.4621 This will be in tomorrow's daily builds. Tom
Hi Tom,
thanks for the answer and sorry for the delay in the reply.
I tried to use the approach you suggested, but my main problems to identify the point where to put the vectors origin.
I hope you can help me
Thanks
giuseppe
Hi Guiseppe,
I guess you are using the Chimera "measure inertia" command to show an inertia ellipsoid for specific atoms. There is not an option to show the principal axes as arrows. I'll add that to our feature request list. But you can do it now by hand if it is worth going to that trouble. You would use Chimera BILD format to draw the axes as in the following mailing list message
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003762.html
but you would use the axes that the measure inertia command reports in the reply log.
Tom
Dear Chimera team, I am using Chimera to create ellipsoids from specific sets of atoms. The ellipsoids are shown in the graphic window as a surface model and information about each ellipsoid are given in the reply log. In it the ellipsoid vectors are reported among others info. I wonder if you have a command to show vectors defining the ellipsoid instead of the surface model in the graphic window. Thanks Regards giuseppe
participants (4)
-
Elaine Meng -
Giuseppe Falini -
Thomas Goddard -
Tom Goddard