Here is a post to color local resolution of cryoEM using Chimera. Similar to coloring map by ChimeraX I posted previously, the concept is same. What we need to prepare is the 3D EM map (sharpened, refined 3D maps or..) and a MRC file with estimated local resolution. The estimated criterion may be FSC=0.5 or FSC=0.143 depending on the software.
When the two MRC files are loaded, in the “volume viewer”, go to “Tools” –> “surface color”, it will pop up a new window (left top one). We have to do the following steps:
- In the “Color Surface” option, select the refined or sharpened map
- Set from by radius to by “volume data value”
- The volume file is the local resolution MRC file.
- Select the Palette, I prefer “blue-red” to stand for stable-unstable color gradient.
- Choose how many colors to be used for the gradient, default is 5 and I prefer 3.
- The volume data values are the estimated ranges of local resolution. A lazy way is clicking “Set” button, then modify the value to a proper range.
- Finally, click “Color” button at the bottom to color the blue-white-red gradient.
The example figure shown above has high resolution (2.5-3.0 Å) in the inner part of “donut”. The outer part of “donut” is averagely 3.0 Å or worse.