Re: [chimerax-users] Color palettes for planes and solid data?
Hi Oli,
The single plane you are showing is the “solid” style, no different from if multiple planes are shown. You can use brightness value 1 for each color if you want, but it needs to be specified, it does not default to 1 (that usually is not what people want when using solid style rendering of more than 1 plane since it would be totally opaque). Also normally single planes are shown as partially transparent in both Chimera 1 and ChimeraX.
Tom
On Feb 28, 2019, at 12:34 PM, Oliver Clarke olibclarke@gmail.com wrote:
I’m also unclear why for an opaque plane it is necessary to set a brightness for each map value - surely a color palette with simple color,value pairs would be fine if there is no transparency issue as there is with a 3D solid representation?
Oli
On Feb 28, 2019, at 3:06 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oli,
To set the colors of different map values use the volume command
volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green
This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel.
When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok.
Tom
On Feb 28, 2019, at 11:35 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi,
Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it!
I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction.
Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached).
Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours).
Cheers Oli
<Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, here is an example of what I mean in Chimera 1. It does clip a cube, but by default it colors the clipped face more or less as I would expect, rather than just producing streaks.
I think it would be useful to be able to use color palettes with equally spaced colors to color planes, and to generate a scale bar for the same. They are informative for density maps, when combined with other representations of the same map. I didn’t realize that the bug report channel was also for feature requests, so I will submit it there.
Oli
On Feb 28, 2019, at 3:48 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oli,
The single plane you are showing is the “solid” style, no different from if multiple planes are shown. You can use brightness value 1 for each color if you want, but it needs to be specified, it does not default to 1 (that usually is not what people want when using solid style rendering of more than 1 plane since it would be totally opaque). Also normally single planes are shown as partially transparent in both Chimera 1 and ChimeraX.
Tom
On Feb 28, 2019, at 12:34 PM, Oliver Clarke olibclarke@gmail.com wrote:
I’m also unclear why for an opaque plane it is necessary to set a brightness for each map value - surely a color palette with simple color,value pairs would be fine if there is no transparency issue as there is with a 3D solid representation?
Oli
On Feb 28, 2019, at 3:06 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oli,
To set the colors of different map values use the volume command
volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green
This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel.
When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok.
Tom
On Feb 28, 2019, at 11:35 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi,
Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it!
I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction.
Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached).
Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours).
Cheers Oli
<Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Oli,
I see. You set the threshold level below all map values which makes a cube, then you clip the cube and color the cap surface. As I mentioned, ChimeraX clip cap surfaces (the flat surface that covers the hole when you clip) does not currently subdivide the triangular mesh, instead producing very long skinny triangles. Since only the vertices of that triangular mesh are colored you just get long streaks of color.
You can submit a ChimeraX feature request (Help / Report a Bug) asking that clip cap subdivision be added like in Chimera 1. You will find many missing features in ChimeraX. It took 4 people 15 years to write Chimera 1, so it will take some time to have all those features in ChimeraX (with our current funding which is 40% of what funded Chimera 1).
Tom
On Feb 28, 2019, at 12:56 PM, Oliver Clarke olibclarke@gmail.com wrote:
Hi Tom, here is an example of what I mean in Chimera 1. It does clip a cube, but by default it colors the clipped face more or less as I would expect, rather than just producing streaks.
I think it would be useful to be able to use color palettes with equally spaced colors to color planes, and to generate a scale bar for the same. They are informative for density maps, when combined with other representations of the same map. I didn’t realize that the bug report channel was also for feature requests, so I will submit it there.
Oli
<PastedGraphic-1.png>
On Feb 28, 2019, at 3:48 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oli,
The single plane you are showing is the “solid” style, no different from if multiple planes are shown. You can use brightness value 1 for each color if you want, but it needs to be specified, it does not default to 1 (that usually is not what people want when using solid style rendering of more than 1 plane since it would be totally opaque). Also normally single planes are shown as partially transparent in both Chimera 1 and ChimeraX.
Tom
On Feb 28, 2019, at 12:34 PM, Oliver Clarke <olibclarke@gmail.com mailto:olibclarke@gmail.com> wrote:
I’m also unclear why for an opaque plane it is necessary to set a brightness for each map value - surely a color palette with simple color,value pairs would be fine if there is no transparency issue as there is with a 3D solid representation?
Oli
On Feb 28, 2019, at 3:06 PM, Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote:
Hi Oli,
To set the colors of different map values use the volume command
volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green
This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel.
When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok.
Tom
On Feb 28, 2019, at 11:35 AM, Oliver Clarke <olibclarke@gmail.com mailto:olibclarke@gmail.com> wrote:
Hi,
Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it!
I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction.
Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached).
Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours).
Cheers Oli
<Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Oliver Clarke -
Tom Goddard