[chimerax-users] Cartoon and ribbon display - change atoms for nucleic acid from C5' to Phosphate

[Tom Goddard]

Hi Bertrand,

  It is currently not possible to change the ribbon spline atoms in ChimeraX.  The specific atoms are set in the C++ code in the get_polymer_spline() routine.

	https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/atomic/atomic_cpp/ribbon_cpp/spline.cpp <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/atomic/atomic_cpp/ribbon_cpp/spline.cpp>

You can put a tube through the P atoms with command

	shape tube @P radius 0.5

Here are some images showing what that looks like compared to a ribbon.

	Tom

Tube through P with backbone atoms, without backbone atom, and with normal C5' ribbon.



> On Jul 31, 2020, at 10:23 AM, bertrand beckert <bertrand.beckert at gmail.com> wrote:
> 
> Dear ChimeraX developper,
> 
> I was wondering if in ChimeraX it is possible to change the atoms used for the cartoon/ribbon display. According to the online user manual (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#top <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#top>) for the nucleic acid the cartoon path seems to be restricted and guided by only the C5'.... could it be possible to change the C5' to the Phosphate instead? is there already a command existing ? 
> 
> Thanks for the nice software!
> 
> Best  regards
> 
> Bertrand
> 
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