[chimerax-users] Ribbon coloring

[F.Xavier Gomis-Rüth]

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
>
>
>
> 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:
>
>> 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
>> -- 
>> <fxgr_signanew.jpg>
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