UCSF Chimera

UCSF Chimera [1] 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. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health National Center for Research Resources (grant 2P41RR001081) and National Institute of General Medical Sciences (grant 9P41GM103311).

Important Notes

Make sure that the appropriate X-window server is running on your computer. It is recommended to use X2Go. Visit HPC Guide to Visual Access for details.
Windows -- middle mouse button workaround (provides for translation via middle mouse button)

Installed Versions

All the available versions of chimera for use can be viewed by issuing the following command. This applies for other applications as well.

module spider chimera

output:

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chimera: chimera/1.13.1

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The default version can be loaded as:

module load chimera

Running Chimera in HPC

From a login node, obtain a compute node resource:

srun --x11 --mem=4gb --pty /bin/bash

Load the Module

module load chimera

Run

chimera &

The GUI window opens. Follow the instructions at the tutorial [2].

References

[1] Chimera Home

[2] Getting Started

[3] Tutorials