Dear ChimeraX Users and Developers, I manage to color my cryoEM maps by local resolution, but can't figure out how to display a scale bar of the color code. Any ideas? Or do I have to go back to Chimera for this? Thanks, Stephan
Hi Stephan, Sorry, ChimeraX does not have a color key tool yet. You could make an image of the color key separately in Chimera as described in this recent post, even if you make the structure figure in ChimeraX (for example to use some of the lighting options that are only in ChimeraX). <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html> We have a list of some of those missing features on the ChimeraX download page, in case you wanted to see what else is on the list. <http://www.rbvi.ucsf.edu/chimerax/download.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2020, at 7:52 AM, Tetter Stephan <tetterst@org.chem.ethz.ch> wrote:
Dear ChimeraX Users and Developers, I manage to color my cryoEM maps by local resolution, but can't figure out how to display a scale bar of the color code. Any ideas? Or do I have to go back to Chimera for this? Thanks, Stephan
Thanks, I' try that then Stephan -------- Ursprüngliche Nachricht -------- Von: Elaine Meng <meng@cgl.ucsf.edu> Datum: Do., 25. Juni 2020, 17:25 An: Tetter Stephan <tetterst@org.chem.ethz.ch> Cc: chimerax-users@cgl.ucsf.edu Betreff: Re: [chimerax-users] Local resolution legend Hi Stephan, Sorry, ChimeraX does not have a color key tool yet. You could make an image of the color key separately in Chimera as described in this recent post, even if you make the structure figure in ChimeraX (for example to use some of the lighting options that are only in ChimeraX). <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html> We have a list of some of those missing features on the ChimeraX download page, in case you wanted to see what else is on the list. <http://www.rbvi.ucsf.edu/chimerax/download.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2020, at 7:52 AM, Tetter Stephan <tetterst@org.chem.ethz.ch> wrote:
Dear ChimeraX Users and Developers, I manage to color my cryoEM maps by local resolution, but can't figure out how to display a scale bar of the color code. Any ideas? Or do I have to go back to Chimera for this? Thanks, Stephan
Hi Stephan, Alternatively, generating a gradient between two colors is relatively easy in common software used to draw figures (PowerPoint, Illustrator or what have you), so you can make the color key this way. In PowerPoint, this can be done by drawing a rectangle and following the instructions here to color the rectangle with a gradient: https://support.microsoft.com/en-us/office/add-a-gradient-color-to-a-shape-1... <https://support.microsoft.com/en-us/office/add-a-gradient-color-to-a-shape-11cf6392-723c-4be8-840a-b2dab4b2ba3e> When you apply the coloring by map value in ChimeraX, the log window will report something like this: Map values for surface "surface": minimum 3.279, mean 3.556, maximum 4.327 You can then use these numbers to label the low end, middle and high end of the color key you made (in PowerPoint, you can do this by following the "Create a custom gradient" section of the documentation I pointed to above). It is very easy with a three-color gradient like blue-white-red (three colors, three values to map to the ends and middle of the gradient). It is probably a bit trickier to do with a rainbow or other multi-color gradient, because I don’t see any way to ascertain that the gradient generated in the figure-drawing program has the same "slope" as the one ChimeraX will use to paint your map. And if the color key doesn’t match what’s painted on the map, well it’s useless. A rainbow gradient is generally best avoided anyway, since it is not readable at all for color-blind readers, and often misleading because of the bright yellow (falsely conveying sharp changes in the data you are depicting with the color gradient, when the changes are actually smooth/continuous). I hope this helps, Guillaume
On 25 Jun 2020, at 17:27, Tetter Stephan <tetterst@org.chem.ethz.ch> wrote:
Thanks, I' try that then
Stephan
-------- Ursprüngliche Nachricht -------- Von: Elaine Meng <meng@cgl.ucsf.edu> Datum: Do., 25. Juni 2020, 17:25 An: Tetter Stephan <tetterst@org.chem.ethz.ch> Cc: chimerax-users@cgl.ucsf.edu Betreff: Re: [chimerax-users] Local resolution legend Hi Stephan, Sorry, ChimeraX does not have a color key tool yet. You could make an image of the color key separately in Chimera as described in this recent post, even if you make the structure figure in ChimeraX (for example to use some of the lighting options that are only in ChimeraX). <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html>>
We have a list of some of those missing features on the ChimeraX download page, in case you wanted to see what else is on the list. <http://www.rbvi.ucsf.edu/chimerax/download.html <http://www.rbvi.ucsf.edu/chimerax/download.html>>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2020, at 7:52 AM, Tetter Stephan <tetterst@org.chem.ethz.ch> wrote:
Dear ChimeraX Users and Developers, I manage to color my cryoEM maps by local resolution, but can't figure out how to display a scale bar of the color code. Any ideas? Or do I have to go back to Chimera for this? Thanks, Stephan
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Guillaume, Stephan, ChimeraX and Chimera use linear interpolation of the RGB color components when coloring using a palette (such as by local resolution), and the Chimera color key likewise uses linear interpolation. So a color gradient made with other software should match if it uses linear interpolation of RGB components. There are other issues like "color profiles" associated with an image that could complicate this. ChimeraX and Chimera do not use color profiles but photoshop / gimp and probably Illustrator care about those -- they can make the colors look quite different. Tom
On Jun 25, 2020, at 9:04 AM, Guillaume Gaullier <guillaume@gaullier.org> wrote:
Hi Stephan,
Alternatively, generating a gradient between two colors is relatively easy in common software used to draw figures (PowerPoint, Illustrator or what have you), so you can make the color key this way. In PowerPoint, this can be done by drawing a rectangle and following the instructions here to color the rectangle with a gradient: https://support.microsoft.com/en-us/office/add-a-gradient-color-to-a-shape-1... <https://support.microsoft.com/en-us/office/add-a-gradient-color-to-a-shape-11cf6392-723c-4be8-840a-b2dab4b2ba3e>
When you apply the coloring by map value in ChimeraX, the log window will report something like this: Map values for surface "surface": minimum 3.279, mean 3.556, maximum 4.327
You can then use these numbers to label the low end, middle and high end of the color key you made (in PowerPoint, you can do this by following the "Create a custom gradient" section of the documentation I pointed to above). It is very easy with a three-color gradient like blue-white-red (three colors, three values to map to the ends and middle of the gradient).
It is probably a bit trickier to do with a rainbow or other multi-color gradient, because I don’t see any way to ascertain that the gradient generated in the figure-drawing program has the same "slope" as the one ChimeraX will use to paint your map. And if the color key doesn’t match what’s painted on the map, well it’s useless. A rainbow gradient is generally best avoided anyway, since it is not readable at all for color-blind readers, and often misleading because of the bright yellow (falsely conveying sharp changes in the data you are depicting with the color gradient, when the changes are actually smooth/continuous).
I hope this helps,
Guillaume
On 25 Jun 2020, at 17:27, Tetter Stephan <tetterst@org.chem.ethz.ch <mailto:tetterst@org.chem.ethz.ch>> wrote:
Thanks, I' try that then
Stephan
-------- Ursprüngliche Nachricht -------- Von: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Datum: Do., 25. Juni 2020, 17:25 An: Tetter Stephan <tetterst@org.chem.ethz.ch <mailto:tetterst@org.chem.ethz.ch>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> Betreff: Re: [chimerax-users] Local resolution legend Hi Stephan, Sorry, ChimeraX does not have a color key tool yet. You could make an image of the color key separately in Chimera as described in this recent post, even if you make the structure figure in ChimeraX (for example to use some of the lighting options that are only in ChimeraX). <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html>>
We have a list of some of those missing features on the ChimeraX download page, in case you wanted to see what else is on the list. <http://www.rbvi.ucsf.edu/chimerax/download.html <http://www.rbvi.ucsf.edu/chimerax/download.html>>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 25, 2020, at 7:52 AM, Tetter Stephan <tetterst@org.chem.ethz.ch <mailto:tetterst@org.chem.ethz.ch>> wrote:
Dear ChimeraX Users and Developers, I manage to color my cryoEM maps by local resolution, but can't figure out how to display a scale bar of the color code. Any ideas? Or do I have to go back to Chimera for this? Thanks, Stephan
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
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participants (4)
-
Elaine Meng -
Guillaume Gaullier -
Tetter Stephan -
Tom Goddard