Chimera-Teaching: Difference between revisions
(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.13 === Author / Dist...") |
|||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 10: | Line 10: | ||
=== Version === | === Version === | ||
1. | 1.16 | ||
=== Author / Distributor === | === Author / Distributor === | ||
| Line 25: | Line 25: | ||
*Version 1. | *Version 1.16, installed in /apps/eb/Chimera/1.16-linux_x86_64 | ||
To use this version of Chimera, please first load the module with | To use this version of Chimera, please first load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml Chimera/1. | ml Chimera/1.16-linux_x86_64 | ||
</pre> | </pre> | ||
| Line 47: | Line 47: | ||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml Chimera/1. | ml Chimera/1.16-linux_x86_64<br> | ||
time chimera --nogui [options] <br> | time chimera --nogui [options] <br> | ||
| Line 59: | Line 59: | ||
sbatch sub.sh | sbatch sub.sh | ||
</pre> | </pre> | ||
=== Documentation === | === Documentation === | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml Chimera/1. | ml Chimera/1.16-linux_x86_64 | ||
chimera --help | chimera --help | ||
Latest revision as of 15:26, 18 January 2024
Category
Bioinformatics
Program On
Teaching
Version
1.16
Author / Distributor
Description
more details at Chimera
Running Program
Also refer to Running Jobs on the teaching cluster
- Version 1.16, installed in /apps/eb/Chimera/1.16-linux_x86_64
To use this version of Chimera, please first load the module with
ml Chimera/1.16-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/1.16-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
Documentation
ml Chimera/1.16-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]
Installation
source code from Chimera
System
64-bit Linux