guillawme/chimerax-viz

Visualizations of macromolecular structures with UCSF ChimeraX

Visualizations made with ChimeraX

This repository contains ChimeraX command files that generate images or movies of molecular structures from the PDB and/or EMDB. Each script or set of scripts is in a directory named after the PDB or EMDB entry used to generate the visualization.

I will update this repository whenever I produce a visualization worth sharing (and from publicly available data).

All of these scripts download files from the PDB and EMDB into ~/Downloads/ChimeraX. They also save one or more image or movie files in the directory from where ChimeraX was started before running the script (if you started ChimeraX from a desktop icon, application launcher or menu item, these files will probably be written in ~/Desktop). They can take a long time to run, and often mobilize a fair amount of resources. Each visualization directory contains a README file explaining how much time the corresponding script took to complete on the computer I ran it on.

All ChimeraX command files in this repository are meant to be run in an empty session, so the recommended way to run them is as follows (in which <VIZ> is the directory of the visualization you want to generate and <script.cxc> is the command file):

cd /path/to/this/repo/<VIZ>
chimerax --exit <script.cxc>

The --exit option offers a slightly faster startup by preventing ChimeraX from checking for updates and doing other things only necessary for an interactive session, and makes ChimeraX quit upon completion of the command file, so you get your shell prompt back.