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Installation

REvoDesign uses its own Package Manager — a graphical installer that runs inside PyMOL. It is not distributed on PyPI.

System Requirements

REvoDesign runs on all major operating systems:

Component Recommended
CPU Intel Core i5 or above
Memory 8 GB or above
Disk 2 GB free minimum
Display 1920×1080 or higher
Software PyMOL 2.5+, Python 3.10+ (3.12 recommended)

Supported operating systems:

  • Windows 10 or later
  • Ubuntu Linux 20.04 or later
  • macOS 12 or later

Install PyMOL

REvoDesign requires PyMOL. We recommend installing the open-source build from conda-forge:

# Install Miniconda first: https://www.anaconda.com/docs/getting-started/miniconda/install
conda create -y -n revodesign python=3.12
conda activate revodesign
conda install -y -c conda-forge pymol-open-source pyqt=5
pymol

If you already have a working PyMOL installation (2.5+), skip this step.

Install REvoDesign Package Manager

  1. Open PyMOL.
  2. Navigate to Plugin → Plugin Manager → Install New Plugin.
  3. Select Install from PyMOLWiki or any URL.

  4. Paste the Package Manager URL:

    https://gist.githubusercontent.com/YaoYinYing/c1e8bfe0fc0b9c60bf49ea04a550a044/raw/REvoDesign_PyMOL.py

  5. Click Fetch and confirm.

PyMOL Plugin Manager
PyMOL Plugin Manager interface
Paste Package Manager URL
Paste the REvoDesign Package Manager URL and click Fetch
Confirm install location
Confirm plugin installation location
  1. The REvoDesign Package Manager appears in the Plugin menu.

Install REvoDesign from the Package Manager

  1. Download the latest release (.zip or .tar.gz) from the GitHub Releases page.
  2. In PyMOL, open Plugin → REvoDesign Package Manager.
  3. Set Source to Local file.
  4. Click ... and select the downloaded archive.
  5. In the Extra section, choose components to install:
    • None — core only (recommended for first-time install)
    • Customized — select specific components from the list
    • Everything — all components except the test suite
  6. Click Install.
Package Manager menu entry
Package Manager appears in the Plugin menu after installation
Package Manager interface
Package Manager main interface
Package Manager — judging installer view
Package Manager judging installer — component selection and install progress

First-time installation

Start with None for the Extra components. You can install additional components later by re-running the Package Manager with Customized.

Using the Repository (Advanced)

Set Source to Repository to install directly from GitHub. You can specify a branch, tag, or commit hash in the Commit field. Use Tag to select from available release tags (click the dropdown after the tags load). Click Refresh GitHub Release tags from the right-click menu if the tag list is stale.

Network Configuration

In the Network section you can configure:

  • HTTP/HTTPS proxy settings
  • PyPI mirror URL (useful for users in mainland China)

Verify Installation

  1. Restart PyMOL after installation completes.
  2. Check that REvoDesign appears in the Plugin menu.
  3. If installation fails, check the PyMOL command log for error details. Users in mainland China may need to adjust network settings and retry.

Right-Click Menu

Right-click in the empty area of the Package Manager for additional options:

Option Description
Upgrade this manager Update the Package Manager UI and Python files. Shows a diff of changes before confirming.
Reset REvoDesign's configuration Delete user config and restore defaults from the program directory. Use when bad config prevents startup.
Collect diagnostic data (reduced) Minimal diagnostic info to clipboard.
Collect diagnostic data (full, non-sensitive) Complete diagnostic info with sensitive data filtered out.
Collect diagnostic data (full, with sensitive) Complete unfiltered diagnostic data. Only share with trusted parties.
Refresh GitHub Release tags Refresh the Tag dropdown for repository installs.
Right-click menu
Right-click menu in the Package Manager
Diagnostic data collection
Diagnostic data collection options

Self-Upgrade

  1. Right-click in the Package Manager empty area.
  2. Select Upgrade this manager.
  3. Review the diff of changes shown in the confirmation dialog.
  4. Click Yes to apply the update.
  5. Restart PyMOL for the updated manager to take effect.

Reset Configuration

If REvoDesign fails to start due to a bad configuration:

  1. Right-click in the Package Manager empty area.
  2. Select Reset REvoDesign's configuration.
  3. Confirm by clicking Yes.
  4. The user config directory is replaced with fresh defaults.
  5. Restart PyMOL.

Advanced Install Options

Option Purpose
Verbose (slider) Logging verbosity during install. Far right = minimal; center = normal; far left = full debug. Use far left for troubleshooting failed installs.
Tag Select a release tag when Source is Repository.
Commit Custom branch, tag, or commit hash for repository installs.
Refresh Refresh the list of available optional components.
Cache Override the default cache location. Not recommended unless disk space is constrained.