<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="">Hi Alexis,<div class=""><br class=""></div><div class=""> You could place markers and link them with the Markers tab of the toolbar. Using the place marker at Point mode then the Move mode you could position it by hand at the center of a ring or on an atom. If you prefer to use calculated positions you could use the "measure center" command on selected atoms of a ring, then use the marker command to place a marker exactly at the reported position.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/tools/markerplacement.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/tools/markerplacement.html</a></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#center" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#center</a></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 5, 2020, at 1:58 PM, Alexis Rohou <<a href="mailto:a.rohou@gmail.com" class="">a.rohou@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi all,<br class=""><div class=""><br class=""></div><div class="">Looking for ideas on how to achieve the following, if possible: </div><div class=""><br class=""></div><div class="">I'd like to draw lines to represent favorable ring-ring stacking interactions (lines between the center of two arene rings), ring-ring edge-to-face interactions (between one atom of one ring and the center of the other ring), and between a regular atom (not part of a ring) and the center of an arene ring.</div><div class=""><br class=""></div><div class="">So I'm guess what I'm looking for is a way to:</div><div class="">1. compute the center coordinates of a ring</div><div class="">2. place an invisible atom there</div><div class="">3. create a pseudobond between this virtual atom and other atoms/virtual atoms</div><div class=""><br class=""></div><div class="">Any suggestions as to how I could achieve this?</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Alexis</div></div>
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