[chimerax-users] Ribbon coloring

[F.Xavier Gomis-Rüth]

Ok, thanks for the info. I will have to keep a functioning version of 
old Chimera then.
Best,
Xavier


On 30/11/22 16:52, Elaine Meng wrote:
> 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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