This is a quick and simple demonstration followed by ChimeraX’s recent Youtube clip. The “surface color” GUI tool is not available in current released version 1.1 but in daily build version.
In ChimeraX version 1.1, to color the local resolution values on our interest molecular map, we use “color” command to color the map.
For example: color sample #1 map #2 palette 2.5,blue:3.5,white:4.5,red
Above command colors local resolution values in map #2 onto map #1 using the user defined blue-white-red gradient palette. I used to use Affinity Photos, powerpoint or Keynote to draw the gradient panel for publication. Now ChimeraX daily build version provides a convenient “surface color” gui to add such color key.
I load map and local resolution estimated map in this ChimeraX daily build. Adjust contour level, remove dust and call the “surface color” function. The surface color can be called from “tools -> “volume data” -> surface color. A surface color panel shows on the right. Users should define maps, color by “volume data value”, choose color gradient and click “color”.
The map now is colored as desired. Simply click the color box to change whatever color we want to use. After that, click “Key” button to pop up another panel and a use “left mouse button” to adjust location/size of the color key in ChimeraX display panel. Then we can save image for further use.