[chimerax-users] [Chimera-users] Coloring model by b-factor

[Elaine Meng]

Minor correction, actually I used the following since the model was #1, not #4:

open 2gbp
hide ribbons
show atoms
color by bfactor /A palette red:green:blue range 35,45

If you meant that you wanted to ONLY color the atoms/residues with bfactor 35-45, then you need something fancier.  For example, to make everything white first:

color white

...then color only the atoms with bfactor 35-45:

color by bfactor /A & @@bfactor>=35 & @@bfactor<=45 palette red:green:blue range 35,45

- OR -

select /A & @@bfactor>=35 & @@bfactor<=45
color by bfactor sel palette red:green:blue range 35,45

The "range" is only defining how the palette colors are spread, not what actually gets colored. The atom-spec defines what actually gets colored.  How to include attribute values in atom-specs:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>

I hope this helps,
Elaine


> On Jul 7, 2022, at 2:18 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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
> 
> 
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