[Chimera-users] [EXTERNAL] Elliptical cylinders

John Hackett John.Hackett at vcuhealth.org
Thu Nov 14 14:43:47 PST 2019

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 at cgl.ucsf.edu<mailto:meng at 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:

For example, the “shape” command can make either of those.

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.

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 at vcuhealth.org<mailto:John.Hackett at 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

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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