<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=""><blockquote type="cite" class=""><div class="">Begin forwarded message:</div><br class="Apple-interchange-newline"><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">Dale Calleja <<a href="mailto:calleja.d@wehi.edu.au" class="">calleja.d@wehi.edu.au</a>><br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Help with new user to ChimeraX training</b><br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">February 22, 2021 at 7:46:56 PM PST<br class=""></span></div><div style="margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">"<a href="mailto:chimerax@cgl.ucsf.edu" class="">chimerax@cgl.ucsf.edu</a>" <<a href="mailto:chimerax@cgl.ucsf.edu" class="">chimerax@cgl.ucsf.edu</a>><br class=""></span></div><br class=""><div class=""><div class="WordSection1" style="page: WordSection1;"><div class="" style="font-size: 12pt; line-height: 12pt; color: rgb(51, 51, 51); font-family: Calibri, sans-serif; margin: 0cm;"><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;">Hi there,<o:p class=""></o:p></span></div><div class="" style="font-size: 12pt; line-height: 12pt; color: rgb(51, 51, 51); font-family: Calibri, sans-serif; margin: 0cm;"><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;"> </span></div><pre class="" style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;">My name is Dale and I’m new to using ChimeraX. Currently I’m trying to use the ‘getting started’ guide for Chimera but a lot of the commands don’t seem to work in my version of ChimeraX (0.93). The most recent example was trying to use the example commands for labelling all lys residues in the hot pink colour. From the ‘Working with commands – Part 1’ part of the guide, the command is <b class="">color hot pink :lys. </b>I always get the error<b class=""> <i class="">Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword</i></b><i class="">. <o:p class=""></o:p></i></span></pre><pre class="" style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";"><i class=""><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;"> </span></i></pre><pre class="" style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;">Can you please explain why this is? Am I copying the command wrong from the ChimeraX user guide?<o:p class=""></o:p></span></pre><pre class="" style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";"><i class=""><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;"> </span></i></pre><pre class="" style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;">Thanks in advance!<o:p class=""></o:p></span></pre><pre class="" style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;"> </span></pre><pre class="" style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span class="" style="font-size: 11pt; font-family: Arial, sans-serif;">Dale.</span></pre></div></div></blockquote><br class="">Hi Dale,<div class="">(For future reference, the correct e-mail address for asking ChimeraX questions is <a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>, CC'd on this reply.)<div class=""><br class=""><div class="">Chimera and ChimeraX are two different programs. You cannot just use Chimera commands in ChimeraX.</div><div class=""><br class=""></div><div class="">See the ChimeraX User Guide:</div><div class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/index.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/index.html</a>></div><div class=""><br class=""></div><div class="">... and ChimeraX tutorials:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimerax/tutorials.html" class="">https://www.rbvi.ucsf.edu/chimerax/tutorials.html</a>></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">
<span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; line-height: normal; border-spacing: 0px; -webkit-text-decorations-in-effect: none;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">-----</div><div class="">Elaine C. Meng, Ph.D. </div><div class="">UCSF Chimera(X) team</div><div class="">Department of Pharmaceutical Chemistry</div><div class="">University of California, San Francisco</div><div class=""><br class=""></div></div></span></div></div></div><br class=""></div></body></html>