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All Projects → smutao → PyVibMS

smutao / PyVibMS

Licence: BSD-2-Clause license
A PyMOL plugin for visualizing vibrations in molecules and solids

Programming Languages

python
139335 projects - #7 most used programming language

Labels

pymol-plugincomputational-chemistrypymolcomputational-physicsquantum-chemistryvibrational-spectroscopytheoretical-chemistry

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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

  1. Page 3

  1. Page 5

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

Linux

Mac OS

Supported quantum chemistry programs

Natively supported

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

Generically supported

The following packages are supported with the help of UniMoVib.

Other analysis tools

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

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