[Chimera] Coloring local resolution

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:

  1. In the “Color Surface” option, select the refined or sharpened map
  2. Set from by radius to by “volume data value”
  3. The volume file is the local resolution MRC file.
  4. Select the Palette, I prefer “blue-red” to stand for stable-unstable color gradient.
  5. Choose how many colors to be used for the gradient, default is 5 and I prefer 3.
  6. 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.
  7. 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.