[Chimera-users] Cylinder coloring extension

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 3 09:39:59 PDT 2019

Hi Thomas,
Chimera “pipes” are always a single color each.

However, our new program ChimeraX has a cylinder-helix representation in which each residue’s segment can be a different color.  Like Chimera, ChimeraX is a free download for noncommercial use. Commands are similar but not identical between the two programs.  


In ChimeraX, if I open 2gbp and from the menu apply preset “cylinders/stubs” and then preset “publication” I get this:

... and then command “color by bfactor palette rainbow” gives this:

Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 3, 2019, at 3:48 AM, Thomas Marcellino <marcellino.tom at gmail.com> wrote:
> Dear Chimera Team,
> I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ?
> Looking forward to an answer,
> Thank you for your time reading my suggestion.
> Thomas M

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