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<font face="Times New Roman, Times, serif">Dear Elaine,<br>
thanks a lot for pointing this out, it is, as you state, a good
solution however partial.<br>
If this is not an issue in old Chimera, it may be implemented at
some point in ChimeraX.<br>
In the meantime, I will have to go back to the old program.<br>
Best,<br>
Xavier<br>
</font><br>
<div class="moz-cite-prefix">On 29/11/22 18:20, Elaine Meng wrote:<br>
</div>
<blockquote type="cite"
cite="mid:EF95058E-F5E9-4038-BE6A-468EF3DAE361@cgl.ucsf.edu">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
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"
src="cid:part1.a44QSUQT.cF8CMRhE@ibmb.csic.es" class=""
width="434" height="640"></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"
src="cid:part2.WalSdJo6.dg6n9wZe@ibmb.csic.es" class=""
width="630" height="347"></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="moz-txt-link-freetext" moz-do-not-send="true">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="">
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class="">
</blockquote>
<br class="">
</div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<img src="cid:part3.7MizLP8L.WnN8oplC@ibmb.csic.es" border="0"></div>
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