Three-Arm Turnstile Assistant

PyMOL plugin to modify molecular structure via turnstile rotation

Why we need this?

We normally adjust molecular structure in terms of bond length, angle and dihedral. However, the present molecular structure editors (e.g. GaussView, Avogadro) cannot handle parameter like this

(animation from https://ukturnstiles.co.uk/)

which is called three-arm turnstile rotation. The fact is that such intramolecular motion is frequently observed in coordination compounds. We provide this tool Three-Arm Turnstile Assistant to help with the computational studies of this motion.

Installation

1. clone this repo by clicking Code -> Download ZIP

2. open PyMOL 2.5+

3. click "Plugin" -> "plugin manager" -> "Install New Plugin" -> "Choose", then choose the "src/__init__.py" file

4. "Turnstile Assistant" will be installed to PyMOL and show up in the "Plugin" drop-in menu

How to use?

Simple case (one atom per arm)

simple.mp4

Substituents on arm

with-substituent.mp4

Note: For each arm, the atom directly bonded to the central anchor atom should be FIRST selected. In this video, the atoms directly bonded to the anchor atom are 31, 53, and 75.

Citation

If you find this tool useful in your research, please cite our articles.

1. Y. Tao, W. Zou, G. Luo, E. Kraka, Describing Polytopal Rearrangement Processes of Octacoordinate Structures. I. Renewed Insights into Fluxionality of the Rhenium Polyhydride Complex ReH₅(PPh₃)₂(Pyridine), Inorg. Chem., 60, 2492 (2021)

2. Y. Tao, X. Wang, W. Zou, G. Luo, E. Kraka, Unusual Intramolecular Motion of ReH₉^2- in K₂ReH₉ Crystal: Circle Dance and Three-Arm Turnstile Mechanisms Revealed by Computational Studies, Inorg. Chem., 61, 1041 (2022)