Worm plots is one of the still missing features.
I probably have the following options (though I haven't actually tried any):
- compute my own spline and place a dense string of spheres - compute my own spline and place alternating spheres and cones - place pseudoatoms and compute a surface with a small probe radius - wait until Chimera's worm plot arrives in ChimeraX.
Or is there a better way?
Thanks! Boris
Hi Boris, In Chimera the worms were a special case of ribbon. It might be possible to use the ribbon path in ChimeraX, but the sticking point may be the lack of user-interface controls to vary ribbon width/height along the path, or even whether that would be possible given the way that ribbons are encoded. Might be possible with python or by altering ChimeraX code, but somebody else would have to advise on that.
Also I don't know if it's any use to you, but you can export worms from Chimera as Collada (.dae) and open the Collada file in ChimeraX -- that looks pretty good, collada file and ChimeraX screenshot attached. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 28, 2020, at 3:20 PM, Boris Steipe boris.steipe@utoronto.ca wrote:
Worm plots is one of the still missing features.
I probably have the following options (though I haven't actually tried any):
- compute my own spline and place a dense string of spheres
- compute my own spline and place alternating spheres and cones
- place pseudoatoms and compute a surface with a small probe radius
- wait until Chimera's worm plot arrives in ChimeraX.
Or is there a better way?
Thanks! Boris
ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Elaine!
The collada solution looks interesting.
Regarding the user interface, I had hoped that e.g. an attribute file could define tube radius at CA positions, with smooth interpolation between.
A python approach would be good as well.
Cheers, Boris
On 2020-10-29, at 08:41, Elaine Meng meng@cgl.ucsf.edu wrote:
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Hi Boris, In Chimera the worms were a special case of ribbon. It might be possible to use the ribbon path in ChimeraX, but the sticking point may be the lack of user-interface controls to vary ribbon width/height along the path, or even whether that would be possible given the way that ribbons are encoded. Might be possible with python or by altering ChimeraX code, but somebody else would have to advise on that.
Also I don't know if it's any use to you, but you can export worms from Chimera as Collada (.dae) and open the Collada file in ChimeraX -- that looks pretty good, collada file and ChimeraX screenshot attached. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<Screen Shot 2020-10-28 at 3.39.39 PM.png>
On Oct 28, 2020, at 3:20 PM, Boris Steipe boris.steipe@utoronto.ca wrote:
Worm plots is one of the still missing features.
I probably have the following options (though I haven't actually tried any):
- compute my own spline and place a dense string of spheres
- compute my own spline and place alternating spheres and cones
- place pseudoatoms and compute a surface with a small probe radius
- wait until Chimera's worm plot arrives in ChimeraX.
Or is there a better way?
Thanks! Boris
ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
<testcollada.dae>
participants (2)
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Boris Steipe -
Elaine Meng