<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Elaine,<div class=""><br class=""></div><div class="">Thanks for this, very helpful! I hadn’t realised that pipes picks up the color from the original model and had been forcing it with helixColor. Can work around using this knowledge.</div><div class=""><br class=""></div><div class="">ChimeraX looks like it’s going to be awesome.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Kyle</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 2 Dec 2016, at 16:07, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Kyle,<div class="">Unfortunately once it’s made, it’s made. Instead you have to get the coloring you want on the original model, and then recreate the pipes (& planks). Each whole pipe would be the same color, though, taken from the ribbon color of the first residue in that helix; it is not divided into independently colorable per-residue segments. The new pipes model should overwrite the existing pipes model, but f you seem to be getting duplicate models, extras can be closed using the Model Panel (under Favorites in the menu). </div><div class=""><br class=""></div><div class="">You could try to “highlight” a position by also displaying the atomic structure CA atom of that residue as a ball or sphere, but I don’t know how well that would meet your needs, sorry.</div><div class=""><br class=""></div><div class="">In our next-gen program ChimeraX, not yet publicly available but will be soon (as early development, not a finished product), </div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimerax/" class="">http://www.rbvi.ucsf.edu/chimerax/</a>></div><div class="">...there are helix “tubes” (like cylinders but curved) that are better integrated with the atomic model and cartoon ribbons, and can be recolored even in per-residue segments after they are shown. Example image with leucine segments in red attached below.</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><span id="cid:C4739FA2-7DDF-49C7-AA70-98490E10895F@gateway.sonic.net"><tube.png></span></div><br class="">On Dec 2, 2016, at 3:40 PM, Kyle Morris <<a href="mailto:kylelmorris@berkeley.edu" class="">kylelmorris@berkeley.edu</a>> wrote:<br class=""><br class=""><blockquote type="cite" class="">Dear Chimera dev,<br class="">I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn’t update the color, only on the original model.<br class="">Thanks for your help!<br class="">Best wishes,<br class="">Kyle<br class="">scription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></blockquote><br class=""></div></div></div></blockquote></div><br class=""></div></body></html>