Installation

Official PyMOL on Windows

1. You must have PyMol installed.
2. Download the latest nightly build of "cbr-tools-202XXXXX-win64.zip" file from the releases section.

3. Open the "Plugin Manager"

4. Select the "Install New Plugin" tab and use the "Choose file" button to find the "pymol-plugins-win.zip" file downloaded in step 2.

5. The CBR PyMol plugins will now run every time your PyMol is started.

Anaconda/Conda Users

This suite is compatible with the open-source PyMol distribution available at conda-forge. However, additional packages must be installed manually as they do not get installed automatically with this distribution. Run the following in your conda terminal to install:

1. Install PyMOL Open-Source

 conda install conda-forge::pymol-open-source

2. Install missing packages

pip install numpy biopython requests

If you are using Linux or MacOS, please see the following section as well.

Troubleshooting

Unlike the official PyMOL release from Schrodinger, the Anaconda version may vary from machine to machine. This makes it impossible to test all possible cases and ensure the plugin will be compatible. If you are running into problems using Anaconda, you can try the following:

Ensure you have the latest version

You can update PyMOL by running the following in your conda terminal:

conda update -c conda-forge pymol-open-source

Linux/MacOS

Currently, there is no official build for Linux and OSX. As the plugin is written in Python, it is possible to run on any platform. However, the following is needed for correct operation of all components:

• The clustalo executable is in your path. Go to the Clustal Omega website for information.
• The cbr-tools-extra executable is needed in your path. This can be obtained at: https://github.com/TUM-CBR/cbr-tools-extra

You can look at the pre-release.yml file to understand how the Windows version is packaged and follow suit on other platforms.

Getting Started

After installing the plugin, the "CBR Tools" option will show up on the PyMol "Plugin" menu item:

Once selected, you will be greeted with the main launcher:

The launcher allows you to access all of the tools available in the plugin by clicking the relevant button. See the "Documentation" section below for information about each of the tools. See the relevant links of the right of this page for additional documentation of the applications.

Nightly Build

Every time a new feature is added to the "CBR Tools" source code, the "Nightly Build" will be updated in the releases page. You are welcome to install that version to test out the latest features. Although we aim to always have functional nightly releases, we anticipate they will contian bugs so use with caution and please report any issues you encounter so the "Official Release" can become better.

The istallation process of a "Nightly Build" is the same as an "Official Release".