CAVER PyMOL plugin

The CAVER PyMOL plugin enables calculation and visualization of tunnels in PyMOL. For the calculation of tunnels, the plugin utilizes CAVER 3.02 software package.

Original Website: https://www.caver.cz

Features of this fork

• Support modern PyMOL driven by PyQt
• Support MD analysis
• Flexibler starting point and residue inclusions
• Results playback
• Extended PyMOL commandline prompt caver_set
• Extended PyMOL commandline prompt caver_tunnel_jump and caver_tunnel_jump_to
• Caver Tunnel Analyst: analyst, visualize, plot (requires matplotlib)
• Tunnel Movie

Image Preview

(A). Refactored pluggin interface. (B). Configuration window. (C). Starting point selection and refines. (D). Starting point from residues, atons or coordinates. (E). Tunnel MD analysis. (F, G). caver_set auto-completion for (E) options and (G) values.

(A) Analyst window for per-tunnel analysis. (B). Tunnels rendered as lines. (C). Timeline view of tunnel evolution. (D). Per-frame view of tunnel. (E). Tunnel plot settings. (F). Publication-quality tunnel Plot.

Movie Preview

Contributors:

• Human Computer Interaction Laboratory Faculty of Informatics, Masaryk University
• Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment Faculty of Science, Masaryk University
• Thomas Holder, Schrodinger Inc.
• Yinying Yao, Huazhong Agricultural University

Requirements

• PyMOL >= 2.5
• OpenJDK

Installation instructions

See the installation instruction for more detailed information.

1. Install OpenJDK

• For macOS: run brew install openjdk in terminal, then add it to PATH according to the instructions output with HomeBrew.

2. Download plugin
3. Start PyMOL
4. Open Plugin manager (Plugin -> Plugin manager)
5. Install plugin (Install new plugin -> Choose file... and select downloaded zip file)
6. Restart PyMOL

License

GNU General Public License, version 3 (GPL-3.0)