Hi,
I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)?
It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc.
It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet.
Cheers
Oli
HI Oli, Thanks for the suggestion. I agree these would be great to have in ChimeraX, and we certainly haven’t ruled it out… but (as you know) many things are vying for developer time. I would certainly use those palettes if they were available.
We’re aware of Colorbrewer and actually its palettes have been in Chimera’s Palette Editor for quite a while: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/palette.html
However, they never got interfaced with coloring by value and the only direct use was for gradient-coloring the background… admittedly not the best use of most multicolor schemes. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 8, 2017, at 8:35 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi,
I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)?
It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc.
It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet.
Cheers Oli
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I wrote some code to add colorbrewer schemes as colormap (palette) names, so they should be available with the "color" and "rainbow" commands (in tomorrow's daily build). Those were the most obvious uses. What are others? If they are easy, we can drop them in.
Conrad
On 9/8/2017 1:20 PM, Elaine Meng wrote:
HI Oli, Thanks for the suggestion. I agree these would be great to have in ChimeraX, and we certainly haven’t ruled it out… but (as you know) many things are vying for developer time. I would certainly use those palettes if they were available.
We’re aware of Colorbrewer and actually its palettes have been in Chimera’s Palette Editor for quite a while: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/palette.html
However, they never got interfaced with coloring by value and the only direct use was for gradient-coloring the background… admittedly not the best use of most multicolor schemes. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 8, 2017, at 8:35 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi,
I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)?
It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc.
It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet.
Cheers Oli
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Conrad that’s fantastic, thanks! The only other case I can think of off hand would be scolor for coloring maps e.g. by local resolution.
Cheers Oli
On 9/10/17, 2:52 AM, "Conrad Huang" conrad@cgl.ucsf.edu wrote:
I wrote some code to add colorbrewer schemes as colormap (palette) names, so they should be available with the "color" and "rainbow" commands (in tomorrow's daily build). Those were the most obvious uses. What are others? If they are easy, we can drop them in.
Conrad
On 9/8/2017 1:20 PM, Elaine Meng wrote: > HI Oli, > Thanks for the suggestion. I agree these would be great to have in ChimeraX, and we certainly haven’t ruled it out… but (as you know) many things are vying for developer time. I would certainly use those palettes if they were available. > > We’re aware of Colorbrewer and actually its palettes have been in Chimera’s Palette Editor for quite a while: > http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/palette.html > > However, they never got interfaced with coloring by value and the only direct use was for gradient-coloring the background… admittedly not the best use of most multicolor schemes. > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Sep 8, 2017, at 8:35 AM, Oliver Clarke olibclarke@gmail.com wrote: >> >> Hi, >> >> I see in the help for the “rainbow” command that there is an option for web-fetched palettes – any chance for integrating support for ColorBrewer ( http://colorbrewer2.org/#)? >> >> It has different very well-designed palettes for sequential (e.g. color by residue) divergent (e.g. color by charge or hydrophobicity) and qualitative (e.g. color by chain) data, and they are designed to be colorblind-safe etc. >> >> It’s intended for cartography, but I have manually used their palettes for structural biology with pleasing results – the full set of palettes can be downloaded as JSON or in an excel spreadsheet. >> >> Cheers >> Oli >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users@cgl.ucsf.edu >> Manage subscription: >> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users@cgl.ucsf.edu > Manage subscription: > http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >
Hi Oli and everybody else,
In the ChimeraX daily build, the ColorBrewer palettes are available with “rainbow” (aka “color sequential”) and with the “color” command “map” option. The latter is the functional equivalent of Chimera’s “scolor” command, coloring by map value.
I realize documentation is needed since the ColorBrewer website doesn’t show the names of the palettes. I plan to have this done today, to be available tomorrow on the website and in the daily build. For now, 3 important notes:
(1) anybody eager to try today can use Chimera to discover the names that could be used in the ChimeraX command line (start Chimera, enter command “start Palette Editor”, choose any relevant options and click the palette of interest)
(2) users should cite: www.ColorBrewer.org, color specifications and designs by Cynthia A. Brewer, Pennsylvania State University.
(3) currently if coloring by map value, you cannot control the exact value-color mapping with palettes from colorbrewer or colourlovers; the colors in the palette are spaced equally along the range of values.
They are quite fun to play with, as I’ve been doing today. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 10, 2017, at 7:57 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi Conrad that’s fantastic, thanks! The only other case I can think of off hand would be scolor for coloring maps e.g. by local resolution.
Cheers Oli
On 9/10/17, 2:52 AM, "Conrad Huang" conrad@cgl.ucsf.edu wrote:
I wrote some code to add colorbrewer schemes as colormap (palette) names, so they should be available with the "color" and "rainbow" commands (in tomorrow's daily build). Those were the most obvious uses. What are others? If they are easy, we can drop them in.
Conrad
I don't think you can "start Palette Editor" in ChimeraX, only in Chimera.
Conrad
On 9/12/2017 1:47 PM, Elaine Meng wrote:
Hi Oli and everybody else,
In the ChimeraX daily build, the ColorBrewer palettes are available with “rainbow” (aka “color sequential”) and with the “color” command “map” option. The latter is the functional equivalent of Chimera’s “scolor” command, coloring by map value.
I realize documentation is needed since the ColorBrewer website doesn’t show the names of the palettes. I plan to have this done today, to be available tomorrow on the website and in the daily build. For now, 3 important notes:
(1) anybody eager to try today can use Chimera to discover the names that could be used in the ChimeraX command line (start Chimera, enter command “start Palette Editor”, choose any relevant options and click the palette of interest)
(2) users should cite: www.ColorBrewer.org, color specifications and designs by Cynthia A. Brewer, Pennsylvania State University.
(3) currently if coloring by map value, you cannot control the exact value-color mapping with palettes from colorbrewer or colourlovers; the colors in the palette are spaced equally along the range of values.
They are quite fun to play with, as I’ve been doing today. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 10, 2017, at 7:57 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi Conrad that’s fantastic, thanks! The only other case I can think of off hand would be scolor for coloring maps e.g. by local resolution.
Cheers Oli
On 9/10/17, 2:52 AM, "Conrad Huang" conrad@cgl.ucsf.edu wrote:
I wrote some code to add colorbrewer schemes as colormap (palette) names, so they should be available with the "color" and "rainbow" commands (in tomorrow's daily build). Those were the most obvious uses. What are others? If they are easy, we can drop them in. Conrad
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Yes, in my message I said you would do that in Chimera. Elaine
On Sep 12, 2017, at 2:46 PM, Conrad Huang conrad@cgl.ucsf.edu wrote:
I don't think you can "start Palette Editor" in ChimeraX, only in Chimera.
Conrad
On 9/12/2017 1:47 PM, Elaine Meng wrote:
Hi Oli and everybody else, In the ChimeraX daily build, the ColorBrewer palettes are available with “rainbow” (aka “color sequential”) and with the “color” command “map” option. The latter is the functional equivalent of Chimera’s “scolor” command, coloring by map value. I realize documentation is needed since the ColorBrewer website doesn’t show the names of the palettes. I plan to have this done today, to be available tomorrow on the website and in the daily build. For now, 3 important notes: (1) anybody eager to try today can use Chimera to discover the names that could be used in the ChimeraX command line (start Chimera, enter command “start Palette Editor”, choose any relevant options and click the palette of interest) (2) users should cite: www.ColorBrewer.org, color specifications and designs by Cynthia A. Brewer, Pennsylvania State University. (3) currently if coloring by map value, you cannot control the exact value-color mapping with palettes from colorbrewer or colourlovers; the colors in the palette are spaced equally along the range of values. They are quite fun to play with, as I’ve been doing today. Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
participants (3)
-
Conrad Huang -
Elaine Meng -
Oliver Clarke