[chimerax-users] Ribbon coloring

[Elaine Meng]

HI Xavier,
The ribbon calculation is completely different in ChimeraX than in Chimera, so my guess is that this part of ChimeraX is unlikely to change.  I thought other programs (Pymol maybe?) also have the coloring that extends beyond the wide part of the ribbons, like ChimeraX, but I understand one may prefer the cleaner look in Chimera. Personally I don't notice it often because I usually don't color coil differently than helix/strand.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 30, 2022, at 2:16 AM, F.Xavier Gomis-Rüth via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Elaine,
> thanks a lot for pointing this out, it is, as you state, a good solution however partial.
> If this is not an issue in old Chimera, it may be implemented at some point in ChimeraX.
> In the meantime, I will have to go back to the old program.
> Best,
> Xavier
> 
> On 29/11/22 18:20, Elaine Meng wrote:
>> Hi Xavier,
>> 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.
>> 
>> See attached screenshot with Chimera image on top, ChimeraX below.
>> 
>> 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
>> 
>> cartoon style ssEnds long
>> 
>> and see if that is good enough for you.
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>> <Screen Shot 2022-11-29 at 8.50.24 AM.png>
>> 
>> 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:
>> <Screen Shot 2022-11-29 at 9.18.18 AM.png>
>> 
>>> On Nov 29, 2022, at 6:57 AM, F.Xavier Gomis-Rüth via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Elaine,
>>> when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil
>>> to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one...
>>> Best,
>>> Xavier
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> 
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