generalized Turnstile Assistant (gTA)

demo.mov

generalized Turnstile Assistant (gTA) is a PyMOL plugin for performing generalized turnstile rotations on molecular structures directly inside the PyMOL GUI.

Dependencies

This plugin requires:

• PyMOL 3.0 or later
• scipy

Installing PyMOL

Open-source PyMOL is available from conda-forge.

Run the following commands in a terminal:

conda create -n pymol-opensource
conda activate pymol-opensource
conda install -c conda-forge pymol-open-source
conda install -c conda-forge scipy
pymol

Installing the Plugin

After launching PyMOL on your computer, open the menu bar and go to Plugin -> Plugin Manager.

In the Plugin Manager dialog:

1. Open the Install New Plugin tab.
2. Click Choose file....
3. Navigate to the gTA plugin folder in this repository.
4. Select __init__.py.
5. Click OK in the remaining pop-up windows.

The plugin is then installed successfully. You should see generalized Turnstile Assistant in the Plugin menu of PyMOL.

How to Use

Workflow

1. Launch PyMOL and load your molecular structure.
2. Open Plugin -> generalized Turnstile Assistant.
3. Click Start.
4. In the PyMOL viewport, click the central atom.
5. Click one connection atom for the first arm.
6. In the PyMOL wizard panel, click Arm Atom Selection Done.
7. Repeat the same process for each additional arm.
8. After selecting at least two arms, click Picking Finished in the plugin window.
9. Use the angle slider to rotate the selected fragment.
10. You can also type a value into the angle box and click Set Angle.
11. Click Revert Changes to return the angle to 0.

What the Plugin Does

• The first picked atom is treated as the central atom.
• For each arm, the first picked atom is used as the arm connection atom.
• After picking is completed, the plugin computes the rotation axis automatically.
• Rotation is then applied directly to the relevant atoms in the loaded PyMOL object.

Current Assumptions

The current implementation assumes:

• only one object is loaded in PyMOL
• the object has only one state
• arm selection requires at least two arms

Reference

If you use this software in your research, please cite:

Tao, Y.; Wang, X.; Zou, W.; Kraka, E. Generalized Turnstile Rotation: Formulation, Visualization, Workflow Implementation, and Application for Modeling Polytopal Rearrangements. Journal of Computational Chemistry 2026, 47, e70432. https://doi.org/10.1002/jcc.70432 Preprint PDF