<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="">This is really simple to do in Python though. The code is:<div class=""><br class=""></div><div class="">from chimera import openModels, Molecule</div><div class="">for m in openModels.list(modelTypes=[Molecule]):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for a in m.atoms:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>a.radius = a.bfactor</div><div class=""><br class=""></div><div class="">If you put the above into a file with a “.py” suffix, you can execute it simply by opening it with the “open” command. Keep in mind that indentation is relevant in Python, so preserve the indentation.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On Sep 13, 2019, at 8:25 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hello Jurgen,<br class="">Sorry, there is no command-line equivalent for the “Radii” section of Render by Attribute, nor is there one for “Worms” — there’s only one for coloring, the “rangecolor” command.<br class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render</a>><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html</a>><br class=""><br class="">Surely it could be done with python scripting, but somebody else would have to advise on that.<br class="">Best,<br class="">Elaine<br 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=""><br class=""><blockquote type="cite" class="">On Sep 12, 2019, at 1:09 PM, Sygusch Jurgen <<a href="mailto:jurgen.sygusch@umontreal.ca" class="">jurgen.sygusch@umontreal.ca</a>> wrote:<br class=""><br class="">Hello,<br class=""> I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. <br class=""><br class=""> In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius).<br class=""><br class=""> What is the command line equivalence for doing this? I cannot seem to find it.<br class=""> Thank you for looking into this.<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>