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<p><font face="Calibri">Wow, thank you very much. </font><br>
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<div class="moz-cite-prefix">On 2019-09-16 6:43 p.m., Eric Pettersen wrote:<br>
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This is really simple to do in Python though. The code is:
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<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>
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<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>
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<div class="">—Eric<br class="">
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<span class="Apple-tab-span" style="white-space: pre;"></span>Eric Pettersen</div>
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<span class="Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab</div>
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<div class="">On Sep 13, 2019, at 8:25 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="" moz-do-not-send="true">meng@cgl.ucsf.edu</a>> wrote:</div>
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<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="">
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<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render" class="" moz-do-not-send="true">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="" moz-do-not-send="true">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html</a>><br class="">
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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="">
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<blockquote type="cite" class="">On Sep 12, 2019, at 1:09 PM, Sygusch Jurgen <<a href="mailto:jurgen.sygusch@umontreal.ca" class="" moz-do-not-send="true">jurgen.sygusch@umontreal.ca</a>> wrote:<br class="">
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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.
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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="">
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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="">
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