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

Non-English Windows users: enable UTF-8 support

This is especially important on Simplified-Chinese Windows, where legacy CMD and Windows PowerShell tools may otherwise use CP936/GBK and produce unreadable output or save downloaded text with the wrong encoding.

1. Press Win+R, enter intl.cpl, and press Enter.
2. Open the Administrative tab.
3. Select Change system locale....
4. Check Beta: Use Unicode UTF-8 for worldwide language support.
5. Select OK and restart Windows when prompted.
6. Open CMD or PowerShell and run chcp. It should report active code page 65001.

Microsoft documents this setting as selecting UTF-8 for the Windows active code page. See Use UTF-8 code pages in Windows apps.

REvoDesign continues to test the default Simplified-Chinese Windows CP936/GBK path. This setting is a recommended interoperability workaround, not a prerequisite or a substitute for reporting encoding problems.

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.

macOS notes

• Use PyMOL Open-Source on native Apple Silicon. The conda-forge build above installs the osx-arm64 binary automatically on Apple Silicon — no Rosetta required. The official PyMOL bundle runs under Rosetta x86_64 emulation and is not recommended; REvoDesign is tested against the native conda-forge build, not the emulated bundle.

• Xcode Command Line Tools are required to compile dependencies that have no prebuilt wheel. Install them once before the first installation:

  xcode-select --install

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 interface

Paste the REvoDesign Package Manager URL and click Fetch

Confirm plugin installation location

1. The REvoDesign Package Manager appears in the Plugin menu.

Install REvoDesign from the Package Manager

Using a Local Archive (Recommended)

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 appears in the Plugin menu after installation

Package Manager main interface

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 in the Package Manager

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.