Chimera-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.13

Author / Distributor

Chimera

Description

more details at Chimera

Running Program

Also refer to Running Jobs on the teaching cluster

• Version 1.13, installed in /usr/local/apps/eb/Chimera/1.13-linux_x86_64

To use this version of Chimera, please first load the module with

ml Chimera/1.13-linux_x86_64

Sample job submission script (sub.sh) to run chimera in a batch job:

#!/bin/bash
#SBATCH --job-name=chimerajob
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=4gb
#SBATCH --time=08:00:00
#SBATCH --output=chimerajob.%j.out
#SBATCH --error=chimerajob.%j.err

cd $SLURM_SUBMIT_DIR

ml Chimera/1.13-linux_x86_64

time chimera --nogui [options]

where [options] need to be replaced by the options you want to use. In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Example of job submission

sbatch sub.sh

Please Note: Currently X-forwarding is not working on the teaching cluster interactive nodes; therefore user can not run an interactive job running Chimera GUI now. We are sorry for the inconvenience.

Documentation

ml Chimera/1.13-linux_x86_64
chimera --help

usage: /usr/local/apps/eb/Chimera/1.13-foss-2016b-linux_x86_64/chimera/share/__main__.py [--help] [--nogui] [-n] [--nostatus] [--silent] [--nomultisample] [--fullscreen] [-f] [--stereo <mode>] [--bgopacity] [--geometry wxh+x+y] [--title title] [--start <extension name>] [--pypath <directory>] [-P <directory>] [--send <file>] [--preferences <file>] [--visual <visual>] [--screen <screen>] [--script <python file>] [--root] [--release] [--version] [--listfiletypes] [--opt] [--debug] [--debug-opengl] [--embed] [--updatecertificates]

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Installation

source code from Chimera

System

64-bit Linux