jarrettsjohnson / amigosiii

Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids

AMIGOS III

Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids

Dependency

AMIGOS III is a plugin to PyMOL version 2.5 or later. It requires matplotlib, pandas and python3.

Installation

Official PyMOL build

If you use an official PyMOL build for Shrondinger, you will need to first check if matplotlib and pandas are available. Launch PyMOL and type in the following command in the PyMOL command prompt:

import matplotlib
import pandas

If the above command complaint that ModuleNotFoundError: No module named 'matplotlib' or ModuleNotFoundError: No module named 'pandas' or use the following command to install matplotlib and pandas respectively:

conda install matplotlib
conda install pandas

You can then download the zip file of AMIGOS III plugin for your operating system (Mac, Windows or Linux) from Releases and install the zip file through the PyMOL Plugin Manager

Open-Source PyMOL on Windows

If you use Christoph Gohlke's Open-Source Pymol on Windows, you will need to install download pre-compiled wheel files for matplotlib and pandas using pip install. After matplotlib and pymol are install, you can install the zip file for AMIGOS III plugin for Windows through the PyMOL Plugin Manager as mentioned above.

PyMOl for a Linux distribution

You can also install AMIGOS III to the PyMOL distributed by your Linux distro. Install pymol, pandas and matplotlib for python3 using the package manager of your distro . Download the zip file for Linux from Releases Launch pymol using root:

sudo pymol

Install the zip file through the PyMOL Plugin Manager. After the installation is completed, you can run PyMOL as a normal user without sudo.

Other systems

If you are using an operating system other than Windows, Mac and Linux, or if your operating system is not 64bit, you will need to manually install AMIGOS III. AMIGOS III includes a C++ program NaTorsion, which can be compiled by

make

or

g++ -O3 NaTorsion.cpp -o NaTorsion -static

The "-static" flag should be removed on Mac OS, which does not support static executable. After the compilation is finished, manually move the AMIGOIII/ folder (i.e., the folder containing this README.md file) to pmg_tk/AMIGOSIII at your pymol installation path.

Reference

Morgan Shine, Chengxin Zhang, Anna Marie Pyle (2022) "AMIGOS III: Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids" Bioinformatics.