<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">If Elaine did not give you enough options, here is one more. You can write an XML Chimera marker file (suffix .cmm) that specifies sphere positions, radii and colors as described in the Chimera documentation that can be read in directly.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles" class="">https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><pre class=""><marker_set name="my spheres">
<marker id="1" x="-6.1267" y="17.44" z="-3.1338" radius="0.35217" r="0" g="1" b="1"/></pre><pre class="">...</pre><pre class=""></marker_set></pre><div class=""><br class=""></div></div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 26, 2022, at 2:16 PM, Elaine Meng via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><br class=""><blockquote type="cite" class="">On May 26, 2022, at 12:48 PM, Elaine Meng via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class=""> [...] make a PDB file where the spheres are fake atoms [...]<br class=""><br class="">However, this would not include your radius values, which would need to be set separately, e.g. with "setattr": <br class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html</a>><br class=""></blockquote><br class="">Correction: a better/easier way than "setattr" to change atomic VDW radii in Chimera is with the "vdwdefine" command:<br class=""><br class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html</a>><br class=""><br class="">Best,<br class="">Elaine<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="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>