How do I colour a sequence by B factor? There's an option to 'Load a sequence coloring file'. Sounds good, but how do I produce an .scf file from a structure coloured by B-factor ? There's a format explanation, but how do I get the actual data ? Grateful for any hints.
Hello, I can't think of any convenient way in ChimeraX to color the sequence (or boxes around sequence letters) by B-factor. The SCF format is normally generated by programs, e.g. JEvTrace and ConSurf Server: <https://www.cgl.ucsf.edu/chimerax/docs/user/formats/scf.html> However, there is a detailed description of the format in the above, so you could generate it "manually" but that would require your own scripting assuming you weren't going to type it into a text editor line by line, which would be very tedious. After coloring by B-factor, you can get a a listing of the resulting colors in the Log with the "info" command. <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html> E.g. if you'd colored ribbon, command: info residues attribute ribbon_color ... would give you the color components in the 0-255 scale used in the SCF format, but it would still be tedious to generate the SCF file. Log contains lines like: [...] residue id /A:393 ribbon_color 169,169,255,255 residue id /A:394 ribbon_color 255,91,91,255 residue id /A:395 ribbon_color 249,249,255,255 [...] In "classic" Chimera (not ChimeraX) you can color the residue letters to match the ribbons, but the lettering can then be very hard to see. In Chimera, you would first color ribbons by residue attribute average bfactor, then show sequence (e.g. from Favorites menu), and then in the Multalign Viewer tool Preferences -> Appearance, you would change the Residue letter coloring "Color scheme" to "ribbon". To make this image I also turned off the display of secondary structure regions in the Region Browser (Multalign Viewer menu Info-> Region Browser). Chimera Multalign Viewer docs: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/f...> Chimera screenshot: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 20, 2024, at 10:38 AM, isaphan--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
How do I colour a sequence by B factor? There's an option to 'Load a sequence coloring file'. Sounds good, but how do I produce an .scf file from a structure coloured by B-factor ? There's a format explanation, but how do I get the actual data ? Grateful for any hints.
Thanks you Elaine for the thorough response, it would be helpful at some point to add in ChimeraX the ability to match the structure coloring scheme with the sequence. I will add this as a new feature request. Regards, Isabelle
On Jun 20, 2024, at 12:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello, I can't think of any convenient way in ChimeraX to color the sequence (or boxes around sequence letters) by B-factor.
The SCF format is normally generated by programs, e.g. JEvTrace and ConSurf Server: <https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/form... >
However, there is a detailed description of the format in the above, so you could generate it "manually" but that would require your own scripting assuming you weren't going to type it into a text editor line by line, which would be very tedious.
After coloring by B-factor, you can get a a listing of the resulting colors in the Log with the "info" command. <https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimerax/docs/user/comm... >
E.g. if you'd colored ribbon, command:
info residues attribute ribbon_color
... would give you the color components in the 0-255 scale used in the SCF format, but it would still be tedious to generate the SCF file. Log contains lines like: [...] residue id /A:393 ribbon_color 169,169,255,255 residue id /A:394 ribbon_color 255,91,91,255 residue id /A:395 ribbon_color 249,249,255,255 [...]
In "classic" Chimera (not ChimeraX) you can color the residue letters to match the ribbons, but the lettering can then be very hard to see. In Chimera, you would first color ribbons by residue attribute average bfactor, then show sequence (e.g. from Favorites menu), and then in the Multalign Viewer tool Preferences -> Appearance, you would change the Residue letter coloring "Color scheme" to "ribbon". To make this image I also turned off the display of secondary structure regions in the Region Browser (Multalign Viewer menu Info-> Region Browser).
Chimera Multalign Viewer docs: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/Contribut... >
Chimera screenshot: <Screenshot 2024-06-20 at 12.03.55 PM.png>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 20, 2024, at 10:38 AM, isaphan--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
How do I colour a sequence by B factor? There's an option to 'Load a sequence coloring file'. Sounds good, but how do I produce an .scf file from a structure coloured by B-factor ? There's a format explanation, but how do I get the actual data ? Grateful for any hints.
participants (3)
-
Elaine Meng -
isaphan -
isaphan＠uw.edu