<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="">Hi, <div class=""><br class=""></div><div class="">I’m using ChimeraX to visualise the structure of a complex of 4 proteins. </div><div class="">I generated a sequence alignment of protein sequences of 1 of the 4 proteins and at each column (amino acid) of the multi protein alignment I assign a score from 0 to 1, where 0 represents no sequence conservation and 1 represent perfect sequence conservation. </div><div class=""><br class=""></div><div class="">I’d like to colour-code these values on a publicly available structure. Can I do it with ChimeraX? I tried to google a bit and read the docs but couldn’t fine a way. </div><div class=""><br class=""></div><div class="">The input “colouring” file could be something like this tab delimited file:</div><div class=""><br class=""></div><div class="">#POS AA <span class="Apple-tab-span" style="white-space:pre"> </span>SCORE</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span> M <span class="Apple-tab-span" style="white-space:pre"> </span>0.2</div><div class="">2 <span class="Apple-tab-span" style="white-space:pre"> </span> V<span class="Apple-tab-span" style="white-space:pre"> </span>0.5</div><div class="">….</div><div class="">n N <span class="Apple-tab-span" style="white-space:pre"> </span>0.8</div><div class=""><br class=""></div><div class="">But I can reshape it in a better format if necessary.</div><div class=""><br class=""></div><div class="">If this is not possible to do it with ChimeraX are you aware of any other tool / software that would allow me to do this?</div><div class=""><br class=""></div><div class="">In the end I’d like to be able to do something like ConSurf (<span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class=""><a href="https://consurf.tau.ac.il" class="">https://consurf.tau.ac.il</a>) </span>does but I’d like to avoid if possible always having to use the web interface as I’d like to semi-automatise this process for every protein in the complex at least.</div><div class=""><br class=""></div><div class="">Thanks a lot!</div><div class="">Best wishes</div><div class="">Nicco</div></body></html>