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Chimera
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Description

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.

Version

Type module avail chimera at the prompt

How to Use

This application requires an X-Windows connection. Further, there are combinations of X11 servers and drivers that cause Chimera to crash. It is known that XQuartz (v2.7.x) is incompatible with Chimera. Users are encouraged to use NX or FastX as their X11 servers.

Chimera uses environment modules. Type

module load chimera

at the prompt. Then type

chimera

Python scripting

Chimera is almost entirely written in python. As such, scripting chimera functions is relatively straightforward. Once a python script is written, it can be run by either including this shebang at the top,

#!/usr/bin/env python2.7

changing the script to executable,

chmod +x myChimeraScript.py

and then running it like so:

./myChimeraScript.py

Or, simply leaving off the shebang and calling the correct python executable:

python2.7 myChimeraScript.py

Here is an example of a chimera python script.

Documentation