<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Xavier,<div class="">In ChimeraX the ribbon shape changes at the CA atom, but the ribbon color changes at the peptide bond; I believe some other programs also do it this way. In Chimera, however, this is not an issue: the color changes at the same place that the ribbon shape changes, at the peptide bond.</div><div class=""><br class=""></div><div class="">See attached screenshot with Chimera image on top, ChimeraX below.</div><div class=""><br class=""></div><div class="">However, there is a partial solution. There is a currently undocumented option in "cartoon style" ... it is "ssEnds long" (default "ssEnds short"). However, this only extends the shape to the peptide bond at the C-terminal end of each helix and strand. There were technical reasons that it did not work for the N-terminal ends, so the option is not very satisfying and that is one reason it is not described in the help page currently. However, you can try</div><div class=""><br class=""></div><div class="">cartoon style ssEnds long</div><div class=""><br class=""></div><div class="">and see if that is good enough for you.</div><div class="">Best,</div><div class="">Elaine<br class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><img apple-inline="yes" id="18097014-6E3F-451F-BDB8-F443DEE1520B" width="434" height="640" src="cid:F35A0FB6-63EE-4674-A751-0D69338725A3" class=""></div><div class=""><br class="webkit-block-placeholder"></div><div class="">In ChimeraX after "cartoon style ssEnds long" the helix shape extends to the peptide bond on the right (C-term end of helix) but not the N-term peptide bond on teh left:</div><div class=""><img apple-inline="yes" id="8C2BE514-04E7-4781-8F68-2FD33A9F5499" width="630" height="347" src="cid:607342D7-571A-4D9E-9AB6-804BBA3F3CBB" class=""></div><br class=""><blockquote type="cite" class="">On Nov 29, 2022, at 6:57 AM, F.Xavier Gomis-Rüth via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi Elaine,<br class="">when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil<br class="">to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one...<br class="">Best,<br class="">Xavier<br class="">-- <br class=""><span id="cid:part1.zeG9lDPV.15TBgr4B@ibmb.csic.es"><fxgr_signanew.jpg></span><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></blockquote><br class=""></div></body></html>