Good morning, is to possible to draw capped elliptical cylinders in Chimera? I would like to render elliptical cylinder representations of nanodiscs together with a membrane protein to visualize results from small-angle scattering experiments. Thanks, -jch ________________________________ John C Hackett, PhD, RPh Associate Professor, Physiology & Biophysics VCU School of Medicine Goodwin Research Laboratory Rm. 165 Massey Cancer Center 401 College St. Richmond, Virginia 23298-0035 Telephone: +1.804.828.5679 ________________________________
Hi John, Sorry, there is no option to create elliptical cylinders per se. However, there may be a devious approach to getting what you want, detailed below. There are several ways to make standard (circular cross-section) cylinders and at least a couple ways to make 3D ellipsoids, as listed here with links: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#objects> For example, the “shape” command can make either of those. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> The ideas I had are: (A) find some other program to create the shape as a VRML file, then open it in Chimera (B) try to fudge it by creating a 3D ellipsoid in Chimera and then using Per-Model Clipping to show only a slab slice of that ellipsoid I tried “B” and it actually looked better than I thought it would. However, it may take some messing around to get the look and size that you want, and then to position it appropriately relative to your membrane protein structure. Here’s what I did to generate what is shown in the attached image. Hard to tell from the image but it is indeed elliptical in cross-section. (1) command: shape ellipsoid radius 5,10,50 color light blue (2) after rotating it around to admire it, reset to initial position, command: reset (3) start Per-Model Clipping, menu: Tools… Depiction… Per-Model Clipping (4) in that dialog, check that the Model is set to the ellipsoid, check “Enable clipping” and “Use slab mode” (changed thickness to 5), clicked “Orient plane” perpendicular to line of sight (5) then rotate with mouse to admire the clipped shape Of course you would use different dimensions and color as desired, and then open your molecule and use the Active checkboxes to freeze one or the other to position them relative to one another. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 14, 2019, at 7:29 AM, John Hackett <John.Hackett@vcuhealth.org> wrote:
Good morning, is to possible to draw capped elliptical cylinders in Chimera? I would like to render elliptical cylinder representations of nanodiscs together with a membrane protein to visualize results from small-angle scattering experiments. Thanks, -jch
Elaine, Thank you very much for your help. , (B) is very clever, although I would need to read about per-model clipping to ensure that I am producing volumes of the correct dimensions. (A) works as well. I was able to generate the volumes in matlab, convert to vrml, then read them into Chimera. I didn't know the latter was possible. Unfortunately, I lose my cylinder caps. Need to figure out why that is. Best, -jch On Nov 14, 2019, at 1:32 PM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi John, Sorry, there is no option to create elliptical cylinders per se. However, there may be a devious approach to getting what you want, detailed below. There are several ways to make standard (circular cross-section) cylinders and at least a couple ways to make 3D ellipsoids, as listed here with links: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#objects<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html*objects__;Iw!632Gf1zpPew!1QNjjblTvlQGsuhx-UuwdTuCwUc4YZMYIzSW4VjWL0yTTb5wtFAW4ZB2eW9OOQDaCg$>> For example, the “shape” command can make either of those. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html<https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html__;!632Gf1zpPew!1QNjjblTvlQGsuhx-UuwdTuCwUc4YZMYIzSW4VjWL0yTTb5wtFAW4ZB2eW_uRpxoqg$>> The ideas I had are: (A) find some other program to create the shape as a VRML file, then open it in Chimera (B) try to fudge it by creating a 3D ellipsoid in Chimera and then using Per-Model Clipping to show only a slab slice of that ellipsoid I tried “B” and it actually looked better than I thought it would. However, it may take some messing around to get the look and size that you want, and then to position it appropriately relative to your membrane protein structure. Here’s what I did to generate what is shown in the attached image. Hard to tell from the image but it is indeed elliptical in cross-section. (1) command: shape ellipsoid radius 5,10,50 color light blue (2) after rotating it around to admire it, reset to initial position, command: reset (3) start Per-Model Clipping, menu: Tools… Depiction… Per-Model Clipping (4) in that dialog, check that the Model is set to the ellipsoid, check “Enable clipping” and “Use slab mode” (changed thickness to 5), clicked “Orient plane” perpendicular to line of sight (5) then rotate with mouse to admire the clipped shape Of course you would use different dimensions and color as desired, and then open your molecule and use the Active checkboxes to freeze one or the other to position them relative to one another. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 14, 2019, at 7:29 AM, John Hackett <John.Hackett@vcuhealth.org<mailto:John.Hackett@vcuhealth.org>> wrote: Good morning, is to possible to draw capped elliptical cylinders in Chimera? I would like to render elliptical cylinder representations of nanodiscs together with a membrane protein to visualize results from small-angle scattering experiments. Thanks, -jch <disc.png> ________________________________ John C Hackett, PhD, RPh Associate Professor, Physiology & Biophysics VCU School of Medicine Goodwin Research Laboratory Rm. 165 Massey Cancer Center 401 College St. Richmond, Virginia 23298-0035 Telephone: +1.804.828.5679 ________________________________
Hi John, If you don't mind hacking Chimera slightly you can make a cylinder with ellipse cross-section. The idea is that the "sop transform" command can scale a surface, but only by the same factor along all axes. But changing one line of code in this file (this is the location on Mac, but you can find it on Linux or Windows) Chimera.app/Contents/Resources/share/Surface/transform.py from stf = ((scale,0,0,0),(0,scale,0,0),(0,0,scale,0)) to stf = ((scale,0,0,0),(0,1,0,0),(0,0,1,0)) makes that command just scale along the screen x axis. So then when I make a cylinder with Chimera command shape cylinder radius 10 height 3 caps true I can stretch it along the x-axis with command sop transform #0 scale 2 You can use the "reset" command to get the cylinder aligned with its x-axis parallel to the screen x-axis before stretching. Tom
On Nov 14, 2019, at 2:43 PM, John Hackett <John.Hackett@vcuhealth.org> wrote:
Elaine, Thank you very much for your help. , (B) is very clever, although I would need to read about per-model clipping to ensure that I am producing volumes of the correct dimensions. (A) works as well. I was able to generate the volumes in matlab, convert to vrml, then read them into Chimera. I didn't know the latter was possible. Unfortunately, I lose my cylinder caps. Need to figure out why that is.
Best, -jch
On Nov 14, 2019, at 1:32 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi John, Sorry, there is no option to create elliptical cylinders per se. However, there may be a devious approach to getting what you want, detailed below.
There are several ways to make standard (circular cross-section) cylinders and at least a couple ways to make 3D ellipsoids, as listed here with links: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#objects <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html*objects__;Iw!632Gf1zpPew!1QNjjblTvlQGsuhx-UuwdTuCwUc4YZMYIzSW4VjWL0yTTb5wtFAW4ZB2eW9OOQDaCg$>>
For example, the “shape” command can make either of those. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html__;!632Gf1zpPew!1QNjjblTvlQGsuhx-UuwdTuCwUc4YZMYIzSW4VjWL0yTTb5wtFAW4ZB2eW_uRpxoqg$>>
The ideas I had are: (A) find some other program to create the shape as a VRML file, then open it in Chimera (B) try to fudge it by creating a 3D ellipsoid in Chimera and then using Per-Model Clipping to show only a slab slice of that ellipsoid
I tried “B” and it actually looked better than I thought it would. However, it may take some messing around to get the look and size that you want, and then to position it appropriately relative to your membrane protein structure.
Here’s what I did to generate what is shown in the attached image. Hard to tell from the image but it is indeed elliptical in cross-section.
(1) command: shape ellipsoid radius 5,10,50 color light blue (2) after rotating it around to admire it, reset to initial position, command: reset (3) start Per-Model Clipping, menu: Tools… Depiction… Per-Model Clipping (4) in that dialog, check that the Model is set to the ellipsoid, check “Enable clipping” and “Use slab mode” (changed thickness to 5), clicked “Orient plane” perpendicular to line of sight (5) then rotate with mouse to admire the clipped shape
Of course you would use different dimensions and color as desired, and then open your molecule and use the Active checkboxes to freeze one or the other to position them relative to one another.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 14, 2019, at 7:29 AM, John Hackett <John.Hackett@vcuhealth.org <mailto:John.Hackett@vcuhealth.org>> wrote:
Good morning, is to possible to draw capped elliptical cylinders in Chimera? I would like to render elliptical cylinder representations of nanodiscs together with a membrane protein to visualize results from small-angle scattering experiments. Thanks, -jch <disc.png>
________________________________ John C Hackett, PhD, RPh Associate Professor, Physiology & Biophysics VCU School of Medicine Goodwin Research Laboratory Rm. 165 Massey Cancer Center 401 College St. Richmond, Virginia 23298-0035 Telephone: +1.804.828.5679 ________________________________
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participants (3)
-
Elaine Meng -
John Hackett -
Tom Goddard