ChimeraX Video Training Project

This project is a training workspace for making capsid videos in UCSF ChimeraX. It is organized like a small GitHub repository with clear notes (.md), reproducible script (.cxc), sessions (.cxs), and renders (.mp4)

ChimeraX Version

The scripts were tested with:

UCSF ChimeraX 1.10.1 (2025-07-24)

Local app used:

/Applications/ChimeraX-1.10.1.app

ChimeraX syntax can change between versions, so use the local manual for this version:

Folder Layout

docs/
  Project notes, tutorials, and feedback

modules/
  README.md

  01_6NJ8_capsid_disassembly/
    source/      Original markdown and reproducibility copy.
    scripts/     ChimeraX .cxc command files.
    sessions/    Generated ChimeraX .cxs sessions.
    renders/     Generated .mp4 movies.

  02_7s20_capsid_exploration/
    source/
    scripts/
    sessions/
    renders/

  03_6NJ8_capsid_symmetry_axes/
    source/
    scripts/
    sessions/
    renders/

Main Files

• Tutorial to render the current preview movie: docs/tutorial_generate_6NJ8_preview_movie.md
• Tutorial to render the 7s20 exploratory preview movie: docs/tutorial_generate_7s20_preview_movie.md
• Tutorial to render the 6NJ8 symmetry-axis preview movie: docs/tutorial_generate_6NJ8_symmetry_axes_video.md
• Notes to share with Abayaa: docs/notes_to_share_with_abayaa.md
• Simpler next-video proposal: docs/proposed_next_simple_video.md
• Detailed technical notes: docs/ChimeraX_1.10.1_project_notes.md

Current Modules

The project is organized as training modules:

1. modules/01_6NJ8_capsid_disassembly/
   • Original 6NJ8 disassembly-style video.
   • Useful for learning how model hierarchy, grouping, and movie timing can fail.
2. modules/02_7s20_capsid_exploration/
   • Same cleanup process applied to the 7s20 structure.
   • Useful for comparison and practice reading ChimeraX scripts.
3. modules/03_6NJ8_capsid_symmetry_axes/
   • Current training module.
   • Keeps the capsid intact and teaches symmetry axes, camera views, fly, roll, wait, and movie encoding.

Important Practices

Use .md files for explanation and .cxc files for ChimeraX commands. Open .cxc files in ChimeraX.

Generated sessions (.cxs) and rendered movies (.mp4) are kept locally but ignored by Git by default. That keeps the future repository lightweight while preserving the scripts needed to regenerate outputs.