lmmentel / colorcif

Render molecular structures from cif files with color coding by symmetry equivalent positions

colorcif.py

A small utility python script to generate high-quality images from cif files with symmetry unique atoms colored with different colors

Dependencies

First make sure you have the following dependencies installed:

• ase
• numpy
• matplotlib

Installation

After downloading and unpacking or cloning the repository run the standard setuptools command

python setup.py install [--user]

Usage

The scipt takes the following optional arguments that can be display with the standard -h flag:

colorcif.py -h

Examples

• color all symmetry unique atoms

colorcif.py TON.cif -o ton_default.pov

• color only T-atoms using RdYlGn colormap from matplotlib

colorcif.py -T -c RdYlGn -o ton_RdYlGn_T.pov TON.cif

• color only oxygen atoms using RdYlBu colormap from matplotlib

colorcif.py -O -c RdYlBu -o ton_RdYlBu_O.pov TON.cif

• color only oxygen atoms using gist_rainbow colormap from matplotlib and rotate the unit cell 30 degrees with respect to each (x, y, z) axes

colorcif.py -O -c gist_rainbow -o ton_gist_rainbow_O.pov -x 30 -y 30 -z 30 TON.cif

• color only oxygen atoms using gist_rainbow colormap from matplotlib and rotate the unit cell 30 degrees with respect to each (x, y, z) axes and the glass texture

  colorcif.py -O -c gist_rainbow -o ton_gist_rainbow_O.pov -x 30 -y 30 -z 30 -t glass TON.cif

  

Additional info

The script is based on the example from the ase documentation.