[Chimera-users] Coloring model by b-factor

[Elaine Meng]

Dear Yang,
I guess you are using ChimeraX (not Chimera) -- the commands are somewhat different between the two programs.  There is also different address for asking ChimeraX questions that you might want to use in the future: chimerax-users at cgl.ucsf.edu  (CC'd here).

As far as I can tell, your ChimeraX command is correct.  I'm not sure why you said it was not working.  Maybe it is because the Log will still tell you the whole range in the structure.  However, the coloring range (different than the value range) will be what you specified in the command.

For example, if I open 2gbp and use

color by bfactor #4/A palette red:green:blue range 35,45

It works correctly.  Although the Log says:
 2575 atoms, 525 residues, atom bfactor range 2 to 63.9

... that is just telling you the values in the structure are 2 to 63.9.  The red-blue-green coloring, however, is spread from 35-45 and everything below 35 is red and everything above 45 is blue.  

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute>

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

> On Jul 7, 2022, at 1:48 PM, 师扬 via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear developer,
> 
> I am trying to color a model by b-facor and used the command like : color by bfactor #4/A palette red:green:blue range 35,45. However, the range setting was not working. So my question is how to color with a user-defined palette and a user-defined range.
> 
> Best wishes,
> Yang