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.
This application requires an X-Windows connection.
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 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 ~]$
A Chimera script contains a series of commands for Chimera. Here is an example of how to run a demo script from the Chimera Scripting Tutorial.
Create a file with the Chimera commands you want to run. In this case, the demo commands will load the Green Fluorescent Protein and display it in various ways. This sample script is available in /usr/local/apps/Chimera/examples/GFP.chimera.
Open a NX session to Biowulf.
biowulf% sinteractive #Start an interactive sesssion on Biowulf salloc: Pending job allocation 48280698 salloc: job 48280698 queued and waiting for resources salloc: job 48280698 has been allocated resources salloc: Granted job allocation 48280698 salloc: Waiting for resource configuration salloc: Nodes cn4271 are ready for job [user@cn4271] cp /usr/local/apps/Chimera/examples/GFP.chimera /home/$USER [user@cn4271] module load chimera [user@cn4271] chimera GFP.chimera &Batch jobMost jobs should be run as batch jobs.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 python2.7changing the script to executable,
chmod +x myChimeraScript.pyand then running it like so:
./myChimeraScript.pyOr, simply leaving off the shebang and calling the correct python executable:
python2.7 myChimeraScript.pyHere is an example of a chimera python script.
Create a batch input file (e.g. Chimera.sh).
#!/bin/bash module load Chimera ./myChimeraScript.pySubmit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] Chimera.sh