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.

References:

• Please see https://www.cgl.ucsf.edu/chimera/docs/credits.html for details on how to cite UCSF Chimera.

• Chimera Documentation
• Chimera Programmer's Guide

• Module Name: Chimera (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• environment variables set
  • LD_LIBRARY_PATH
  • PYTHONPATH
• Reference data in /pdb

This application requires a graphical connection.

Chimera will not run normally on GPU nodes. Chimera can only run on CPU-only nodes

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load Chimera
[user@cn3144 ~]$ chimera &

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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.

Create a batch input file (e.g. Chimera.sh).

#!/bin/bash
module load Chimera
./myChimeraScript.py

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] Chimera.sh