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Revision as of 08:21, 14 October 2009 (view source) Igchoi (Talk | contribs) ← Older edit		Revision as of 04:42, 15 October 2009 (view source) Igchoi (Talk | contribs) (→X-ray crystallography) Newer edit →
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	==X-ray crystallography==		==X-ray crystallography==
-	#[[Molecular replacement]]	+	*Programs
		+	**Installed at ''panflam'' (linux machine; 2 CPU (8 cores))
		+	<pre>/home/x-ray</pre>
		+	**CCP4 1.6.2
		+	***add a line into your .cshrc
		+	<pre>source /home/x-ray/ccp4_1.6.2/include/ccp4.setup</pre>
		+	**CNS_solve 1.2
		+	<pre>source /home/x-ray/cns_solve/cns_solve.env</pre>
		+
		+	*[[Molecular replacement]]
		+
	==Computing resources==		==Computing resources==
	#[[Compbio]]		#[[Compbio]]

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Revision as of 04:42, 15 October 2009

Contents 1 Protocols 2 Part list 3 X-ray crystallography 4 Computing resources 5 Unix & Programming 5.1 Unix 5.2 Python 5.3 Applications 6 Windows

Protocols

1. Molecular biology
2. Protein biochemistry
3. Chemistry

Part list

1. Plasmids
2. Strains
3. Parts Registry

X-ray crystallography

• Programs
  • Installed at panflam (linux machine; 2 CPU (8 cores))

/home/x-ray

• • CCP4 1.6.2
    • add a line into your .cshrc

source /home/x-ray/ccp4_1.6.2/include/ccp4.setup

• • CNS_solve 1.2

source /home/x-ray/cns_solve/cns_solve.env

• Molecular replacement

Computing resources

1. Compbio
2. Microbio
3. Panpyro
4. Panflam

Unix & Programming

Unix

• Installing Compilers
• SSH - how to connect the Lab. PC from your home
• X11 connection
  • Easy safe way is to use SSH's X forwarding:

ssh -X me@remotemachine

• Your display will look to the remote machine like:

echo $DISPLAY
localhost:10.0
firefox --display=$DISPLAY &

xhost/export DISPLAY

• On your local machine:

xhost + remotemachine

• On the remote machine:

export DISPLAY=localhost:0.0

• After you're done, remove remote machine access from your xhost:

xhost -

• SCIM - Input Hangul
• Linux (Unix) commands
• The Linux Document Projects - Numerous useful documents & tutorials are available
• Change locale (language) for 'panpyro'

bash shell:
export LC_ALL=en_GB.ISO8859-1
export LANG=en_GB.ISO8859-1

Python

• BE.180 Biological Engineering Programming - Synthetic biology@MIT Check "Unix&Python" tutorials!
  • Python Cheat Sheet
  • Unix&Python tutorial

Applications

• MySQL
• Matlab
• R-project

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• Hypergraph: EC class

Windows

• MS-Word - 편집시 변경내용 추적