Chimera / ChimeraX
Overview
UCSF Chimera is a highly extensible program for interactive visualisation 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 is the legacy application that is no longer under active development. ChimeraX is now the next-generation molecular visualization program from the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI), that replaces Chimera. RBVI strongly encourages users to now use ChimeraX.
For a detailed, up to date comparison between the two programs please read the UCSF ChimeraX vs. Chimera page.
Restrictions on use
The licence for Chimera and ChimeraX is the same and is restricted to non-commercial purposes. In order to use Chimera/ChimeraX you will need to be added to the relevant group.
A copy of the Chimera license agreement can be found here:
https://www.cgl.ucsf.edu/chimera/license.html
A copy of the ChimeraX license agreement can be found here:
https://www.rbvi.ucsf.edu/chimerax/docs/license.html
In order to use this software, please read the relevant license and then complete our help form to indicate you agree to the licence restrictions.
Set up procedure
In order to use ChimeraX you will need to load the ChimeraX module:
# ChimeraX: this is the recommended module module load apps/binapps/chimerax/1.11.1 # uses python 3.11 # Chimera: old installation that currently does not work on the CSF3 module load apps/binapps/chimera/1.13.1 # uses python 2.7
Chimera legacy depends on old libraries, currently missing from the CSF3’s updated Operating System. If this is required for backwards compatibility reasons or because of a missing essential feature from ChimeraX, please contact us via our help form and we may try to find a solution.
Running the application interactively
ChimeraX is mainly an interactive graphical application. It should not be run on the login node, rather it should be run on one of the interactive nodes.
If using a terminal to log-in the CSF3, make sure that in your ssh command you used the -X flag like:
ssh -X username@csf3.itservices.manchester.ac.uk
Then request an interactive session, and when logged in the compute node load the module and run the app:
# in this example a 2hr session with 4 CPU cores @login1[csf3]$ srun-x11 -p interactive -t 0-2 -n 1 -c 4 @nodeXXX[csf3]$ module load apps/binapps/chimerax/1.11.1 @nodeXXX[csf3]$ chimerax &
In the official documents you can read more about startup options and about all the command line options.
At the bottom of the main window there is a useful command line interface (CLI) where you can type commands. For example typing help opens a window with the documentation.
Please note that ChimeraX is designed to take advantage of a GPU for rendering, using OpenGL. Unfortunately, using the CSF3 GPUs for rendering remotely is not possible with the current CSF3 setup. Therefore rendering performance may be very slow and increasing the number of requested CPUs most probably will not help.
With regards to computation performance, ChimeraX may be able to leverage more than one CPU core in some specific functions like surface and area calculations and volume data processing.
Using Toolshed, a web repository of ChimeraX bundles
The UCSF ChimeraX Toolshed is a web repository of ChimeraX bundles hosted by the UCSF RBVI. A bundle is a separately installable and updatable module that may include tools, commands, command-line specifiers, and/or file format support.
You can open the Toolshed from the Menu: Tools -> See more...
Then you can select a module and install it using the web interface.
Or you can use the toolshed …command to list, install and uninstall bundles
As the modules are written in python, they are installed by default in your $HOME directory in:
~/.local/share/ChimeraX/1.11/lib/python3.11/site-packages
Further info
ChimeraX will use by default the following directories in $HOME, to store its data:
~/.local/share/ChimeraX # python modules, ChimeraX bundles and other data ~/.config/ChimeraX # settings ~/.cache/ChimeraX # cache