<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi John,<div class=""><br class=""></div><div class=""> 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)</div><div class=""><br class=""></div><div class=""> Chimera.app/Contents/Resources/share/Surface/transform.py</div><div class=""><br class=""></div><div class="">from</div><div class=""><br class=""></div><div class=""> stf = ((scale,0,0,0),(0,scale,0,0),(0,0,scale,0))</div><div class=""><br class=""></div><div class="">to </div><div class=""><br class=""></div><div class=""><div class=""> stf = ((scale,0,0,0),(0,1,0,0),(0,0,1,0))</div><div class=""><br class=""></div><div class="">makes that command just scale along the screen x axis. So then when I make a cylinder with Chimera command</div><div class=""><br class=""></div><div class=""> shape cylinder radius 10 height 3 caps true</div><div class=""><br class=""></div><div class="">I can stretch it along the x-axis with command</div><div class=""><br class=""></div><div class=""> sop transform #0 scale 2</div><div class=""><br class=""></div><div>You can use the "reset" command to get the cylinder aligned with its x-axis parallel to the screen x-axis before stretching.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><img apple-inline="yes" id="06335187-8ACB-42E0-AD3E-A5D8C360F6E2" src="cid:FF0585F0-3606-4EE8-9EA6-3689603F4787@cgl.ucsf.edu" class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 14, 2019, at 2:43 PM, John Hackett <<a href="mailto:John.Hackett@vcuhealth.org" class="">John.Hackett@vcuhealth.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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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.
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<div class="">Best, -jch<br class="">
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<div class="">On Nov 14, 2019, at 1:32 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
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Hi John,
<div class="">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.</div>
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<div class="">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:</div>
<div class=""><<a href="https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html*objects__;Iw!632Gf1zpPew!1QNjjblTvlQGsuhx-UuwdTuCwUc4YZMYIzSW4VjWL0yTTb5wtFAW4ZB2eW9OOQDaCg$" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#objects</a>></div>
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<div class="">For example, the “shape” command can make either of those.</div>
<div class=""><<a href="https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html__;!632Gf1zpPew!1QNjjblTvlQGsuhx-UuwdTuCwUc4YZMYIzSW4VjWL0yTTb5wtFAW4ZB2eW_uRpxoqg$" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html</a>></div>
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<div class="">The ideas I had are:</div>
<div class="">(A) find some other program to create the shape as a VRML file, then open it in Chimera</div>
<div class="">(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</div>
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<div class="">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.</div>
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<div class="">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.</div>
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<div class="">(1) command: shape ellipsoid radius 5,10,50 color light blue</div>
<div class="">(2) after rotating it around to admire it, reset to initial position, command: reset</div>
<div class="">(3) start Per-Model Clipping, menu: Tools… Depiction… Per-Model Clipping</div>
<div class="">(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</div>
<div class="">(5) then rotate with mouse to admire the clipped shape</div>
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<div class="">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.</div>
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<div class="">Best,</div>
<div class="">Elaine</div>
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<div class="">-----<br class="">
Elaine C. Meng, Ph.D.<br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
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<blockquote type="cite" class="">On Nov 14, 2019, at 7:29 AM, John Hackett <<a href="mailto:John.Hackett@vcuhealth.org" class="">John.Hackett@vcuhealth.org</a>> wrote:<br class="">
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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<br class="">
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