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UCSF Chimera

An interactive molecular visualization and modeling program.

Homepage Version(s): 1.19

UCSF Chimera requires an environment module

In order to use UCSF Chimera, you must first load the appropriate environment module: 

module load chimera

This application is available in Open OnDemand.

UCSF Chimera is an interactive molecular modeling and visualization program developed by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). It is widely used for visualizing molecular structures, density maps, and trajectories, and for exploratory analysis in structural biology, chemistry, and materials science.

Running Chimera on RCC#

Because Chimera is a graphical application, it should be run using the RCC Desktop via Open OnDemand (OOD). Running Chimera directly on login nodes without a graphical session is not supported.

Launch an RCC Desktop Session#

  1. Log into Open OnDemand
  2. In the top navigation bar, select "Interactive Apps" and then from the drop down, "RCC Desktop".
  3. Select the Slurm Account/partition that you want to use for your job. If you leave this blank, the app will run in our genacc_q account.
  4. Fill out the rest of the job submission form.
  5. Click "Launch" to queue your job.
  6. When your interactive job has started, click Launch.
  7. A new tab will open, and the RCC Desktop will launch shortly after.

Once the session starts, a Linux desktop environment will open in your browser.

Start Chimera#

Open a terminal within the OOD Desktop and run:

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$ module load chimera
$ chimera

The Chimera GUI will launch in a new window.