Thank you very much Elaine ! I actually forgot two very useful options for color byattribute range full and/ or ave residues # ?? it seems to me that with it we do not need to indicate the range values at all .. Enrico Il giorno mer 30 ago 2023 alle ore 19:00 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, You can use as many color,value pairs as you want by specifying them directly in the command. You don't need to use one of the pre-defined palette names. See the color command palette options and ways of specifying colors:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html>
For example:
color byattribute bfactor palette "2.5,cornflower blue:10.3,gold:80.8,red" color byattribute bfactor palette 2.5,#b22222:5.9,#dc143c:15,#ff0000:25.3,#ffff00:46,#adff2f
(where the top palette is enclosed in quotation marks because it contains a space)
Or use the graphical interface of Render by Attribute (available in version 1.6) where you can add as many control points as you like, move them on the histogram, and change their colors using the system color editor. It's in the menu under Tools... Structure Analysis. Choose attributes of "atoms", attribute "bfactor"
See Render by Attribute help for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html>
Then when you apply the Render by Attribute coloring it will show the corresponding command in the Log. If you wanted to script it, that is an easy way of finding out the command.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 30, 2023, at 5:34 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am using ChimeraX to color pdb file according to its structural flexibility determined in the b-factor column
color byattribute bfactor palette rainbow range 2,100
This info is taken directly from the rmsf calculations of short MD trajectory and stored in a single pdb structure in the b-factor column.
Technically It works very well, however in the case of flexible systems, the most of the structures is colored in "red". I enclose a screenshot of an example image along with the corresponded rmsf chart.
Would it be possible to define the gradient of the coloring in more accurate fashion in order that the red zones could have more shades ?
I believe this could be fine-tuned via the "range 2, 100 " attribute and / or switching to other palettes e.g. 'Paired-12' , which naturally has more shades compared to 'rainbow' ..
I would be grateful for any further suggestions !
Yours with thanks,
Enrico