To display NMR ensemble structure in PyMOL, we can use “line” mode to show the aligned 20 (or more) structures. By using the “line” mode, the structural convergence can be easily observed. Often, the tails and the loops are not well aligned, showing large displacements in the aligned ensemble. I have some posts about it.

How to make a similar figure using ChimeraX? When user loads/opens the NMR ensemble file, ChimeraX displays all structure in the default “Cartoons” mode. Here is an example using “rainbow” color scheme.

The “Atoms” mode in ChimeraX displays bonds, like the “ribbon” or “line” mode in PyMOL. What we should do is to hide the sidechain atoms, and the backbone oxygens and hydrogens. One more step is to reduce the “stick radius” as the default bond stick is too thick to show the structural convergence or inconsistency. The default bond size is 0.2 Å and I prefer 0.05 Å for NMR ensemble illustration. Here are the examples using 0.2 (left) and 0.05 Å (right) bond size.

Simply copy the commands below and paste to ChimeraX, the NMR ensemble will be displayed.

hide cartoons
rainbow
show atoms
hide sideonly atoms
hide O atoms
hide H atoms
size stickRadius 0.05
## more lighting setting
lighting shadows false
lighting simple
graphics silhouettes width 1 depthJump 0.01 color grey