Chimera-Teaching - Revision history

Shtsai at 00:22, 5 April 2026

2026-04-05T00:22:19Z

← Older revision		Revision as of 20:22, 4 April 2026
Line 1:		Line 1:
	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==

	1.16		1.16

	=== Author / Distributor ===		== Author / Distributor ==

	[https://www.cgl.ucsf.edu/chimera/ Chimera]		[https://www.cgl.ucsf.edu/chimera/ Chimera]

	=== Description ===		== Description ==

	more details at [https://www.cgl.ucsf.edu/chimera/ Chimera]		more details at [https://www.cgl.ucsf.edu/chimera/ Chimera]

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]
Line 60:		Line 60:
	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
Line 71:		Line 71:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	source code from [https://www.cgl.ucsf.edu/chimera/download.html Chimera]		source code from [https://www.cgl.ucsf.edu/chimera/download.html Chimera]

	=== System ===		== System ==

	64-bit Linux		64-bit Linux

Shtsai: /* Documentation */

2024-01-18T20:26:43Z

Documentation

← Older revision		Revision as of 16:26, 18 January 2024
Line 63:		Line 63:

	<pre class="gcommand">		<pre class="gcommand">
	ml Chimera/1.13-linux_x86_64		ml Chimera/1.16-linux_x86_64
	chimera --help		chimera --help

Shtsai: /* Running Program */

2024-01-18T20:25:55Z

Running Program

← Older revision		Revision as of 16:25, 18 January 2024
Line 25:		Line 25:


	*Version 1.13, installed in ~~/usr/local~~/apps/eb/Chimera/1.13-linux_x86_64		*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/1.13-linux_x86_64		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/1.13-linux_x86_64<br>		ml Chimera/1.16-linux_x86_64<br>

	time chimera --nogui [options] <br>		time chimera --nogui [options] <br>
Line 58:		Line 58:
	<pre class="gcommand">		<pre class="gcommand">
	sbatch sub.sh		sbatch sub.sh
	</pre>		</pre>

	=== Documentation ===		=== Documentation ===

Chelsea: /* Version */

2024-01-18T15:06:09Z

Version

← Older revision		Revision as of 11:06, 18 January 2024
Line 10:		Line 10:
	=== Version ===		=== Version ===

	1.13		1.16

	=== Author / Distributor ===		=== Author / Distributor ===
Line 58:		Line 58:
	<pre class="gcommand">		<pre class="gcommand">
	sbatch sub.sh		sbatch sub.sh
	</pre>		</pre>

	'''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 ===		=== Documentation ===

Shtsai: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.13 === Author / Dist..."

2019-01-25T19:04:34Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.13 === Author / Dist..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===

1.13

=== Author / Distributor ===

[https://www.cgl.ucsf.edu/chimera/ Chimera]

=== Description ===

more details at [https://www.cgl.ucsf.edu/chimera/ 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
<pre class="gscript">
ml Chimera/1.13-linux_x86_64
</pre>

Sample job submission script (sub.sh) to run chimera in a batch job:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=chimerajob 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=4gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=chimerajob.%j.out 
<nowiki>#</nowiki>SBATCH --error=chimerajob.%j.err 

cd $SLURM_SUBMIT_DIR 

ml Chimera/1.13-linux_x86_64 

time chimera --nogui [options] 

</div>
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
<pre class="gcommand">
sbatch sub.sh
</pre>

'''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 ===

<pre class="gcommand">
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]
</pre>

[[#top|Back to Top]]

=== Installation ===

source code from [https://www.cgl.ucsf.edu/chimera/download.html Chimera]

=== System ===

64-bit Linux