maskChains

maskChains is a ChimeraX bundle bundle that adds a command maskChains to ChimeraX that lets you generate a mask to keep all voxels closer to the target protein chain(s) than other chains, including the voxels corresponding to the protein backbone/sidechains and those non-proteinaceous voxels around the protein. This is in contrast to the Surface Zone tool/command in ChimeraX that lets the user specify a distance limit to include voxels near the selected protein chains.

Example: EMD_3741 masked with chain E,F of PDB-5o3l:

Installation

In ChimeraX, go to Tools menu and select More Tools to open the Chimerax Toolshed, find maskChains and click the Install button.

Alternatively, you can install it following these steps:

• Download the ChimeraX_maskChains-1.4-py3-none-any.whl file in the dist folder of this repository
• In the ChimeraX Command input box at the bottom of the display window, run this command
  toolshed install <path/to/the/downloaded/whl/file>

Usage

In the ChimeraX Command input box, run this command
maskChains #1 model #2 chainIds E,F

In this command,

• #1 is the model ID of your density map, change it to the model ID in your ChimeraX session
• #2 is the model ID of your atomic model that is superimposed into the map. Change it to the actual model ID in your ChimeraX session
• E,F are the chain IDs of your target chains for masking. You can specify one or more chain IDs. For amyloids, the chain IDs of the central layer are typically specified here. Your atomic model should have at least one layer above and one layer below your target layer

The ChimeraX commands below would reproduce the image above:

close all
open 3741 from emdb
open 5o3l
maskChains #1 model #2 chainIds E,F
hide #1
hide #2
hide #3
show #3/E,F
style #3/E,F stick
volume #4 level 0.017
color #4 #ffffb2bf
windowsize 800 400
camera ortho
view orient
turn z -30
zoom 1.5
save emd-3741_pdb-5o3l_chain-EF_thresh-0.017.png

Citation

The maskChains tool was developed for our cryo-EM project on the structures of amyloids. If you find maskChains useful, please cite this reference:

M. R. Hoq*, A. Fernandez*, F. S. Vago*, G. I. Hallinan, S. R. Bharath, D. Li, K. A. Ozcan, H. J. Garringer, W. Jiang*, R. Vidal*, B. Ghetti*, Cryo-EM structures of cotton wool plaques' amyloid β and of tau filaments in dominantly inherited Alzheimer disease. Acta Neuropathol. 148, 20 (2024).