PyVibMS

A PyMOL plugin for visualizing vibrations in molecules and solids

Updates

Oct 22, 2021 - Bug fix

May 8, 2021 - Add example for BDF

May 5, 2021 - Add examples for UniMoVib which can generate XYZ and mode files for PyVibMS

May 3, 2021 - Add support for ORCA 4 and Q-Chem 4/5

May 2, 2021 - Add support for Prof. Grimme's xtb program

User Guide

介绍PyVibMS使用的中文文章 请前往 http://bbs.keinsci.com/thread-22835-1-1.html

Our paper on PyVibMS is now published. 🎉

PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids, Journal of Molecular Modeling, 2020, 26, 290. (full text also available at https://sites.smu.edu/dedman/catco/publications/pdf/434.pdf)

This paper serves as a detailed manual of PyVibMS and a few typographical errors need to be corrected:

1. Page 2

<img src="https://raw.github.com/smutao/PyVibMS/master/for-readme/misprint/1.png" width="450">

2. Page 3

<img src="https://raw.github.com/smutao/PyVibMS/master/for-readme/misprint/2.png" width="450">

3. Page 5

<img src="https://raw.github.com/smutao/PyVibMS/master/for-readme/misprint/3.png" width="450">

Installation

1. Please install PyMOL 2.x and download the zip file of this repository

2. Open PyMOL 2.x

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

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

PyVibMS runs on various operating systems.

Windows

<img src="https://raw.github.com/smutao/PyVibMS/master/gallery/pyvibms_on_win10.png" width="750">

Linux

<img src="https://raw.github.com/smutao/PyVibMS/master/gallery/pyvibms_on_centos.png" width="750">

Mac OS

<img src="https://raw.github.com/smutao/PyVibMS/master/gallery/pyvibms_on_macos.png" width="750">

Supported quantum chemistry programs

Natively supported

• Gaussian 09/16
• ORCA 4/5/6
• xtb
• Q-Chem
• CRYSTAL17
• VASP

Generically supported

The following packages are supported with the help of UniMoVib.

• Adf
• BDF
• CFour
• Columbus
• CP2k
• Dalton
• deMon2k
• Dmol3
• Firefly
• Gamess
• Gamess-UK
• Molcas and OpenMolcas
• Molpro
• Mopac
• NWChem
• Pqs
• Psi4
• Turbomole
• Quantum ESPRESSO
• DFTB+
• and more

Other analysis tools

• LModeA
• Phonopy

Tips

• When using the open-source version of PyMOL, one may find it difficult to export the vibration animation directly as a GIF or QuickTime movie due to the missing encoder, a work-around is to export the animation as "PNG images" (by clicking "File"->"Export Movie As"->"PNG Images..."). Then one can use a third-party tool like ezgif to combine these PNG images as animated GIF image.
  Here is an example <img src="https://raw.github.com/smutao/PyVibMS/master/gallery/animations/gif-format.gif" width="350">