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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 Computing resources 7 Unix & Programming 7.1 Unix 7.2 Python 7.3 Applications 8 Windows

Protocols

• Molecular biology
• Protein biochemistry
• Chemistry

Part list

• Plasmids
• Strains
• Parts Registry

X-ray crystallography

• Related programs are installed at panflam (linux machine; 2 CPU (8 cores))

/home/x-ray

• Environment Setup (for tcsh shell) - panflam
• Check your login SHELL

echo $SHELL
/bin/tcsh  # you should see this if you use 'tcsh'

• then, modify your shell enivironment - add followings into .cshrc file in your home directory

# x-ray setting
setenv XRAY /home/x-ray
## CNS
source $XRAY/cns_solve_1.2/cns_solve_env
## phenix
source $XRAY/phenix-1.5-2/phenix_env
## ccp4
source $XRAY/setup-scripts/csh/ccp4.setup
source $XRAY/setup-scripts/csh/ccp4-others.setup

• activate the enivronment

source ~/.cshrc

• panpyro - cluster

# x-ray
# phenix 11-07-2009
source /home/x-ray/phenix-1.5.2/phenix-1.5-2/phenix_env
# ccp4
source /home/x-ray/ccp4/setup-scripts/csh/ccp4.setup
source /home/x-ray/ccp4/setup-scripts/csh/ccp4-others.setup

• running phenix by 'qsub' on multiple processers panpyro
• EXAMPLE

# swissmodel superimposed to 1V19 MR solution
phenix.autobuild ../MR.1_copy.mtz ../swissAB.pdb seq_file=../sde2656.fas run_command="qsub -q infi" background=False nproc=5 nbatch=5 >& job.log &
phenix.automr ../pointless_sde2656_1_001_scala1-2.6A.mtz ../MR2_1V19_polyALA.pdb seq_file=../sde2656.fas copies=2 identity=25 run_command="qsub -q infi" background=False nproc=5 nbatch=5 >& job.log & 

• X-ray programs
• Methods
  • 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

• check ssh_config & sshd_config (/etc/ssh/) by SSH

X11Forward yes

• old way - no need to follow

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

---

• Hypergraph: EC class

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

• check ssh_config & sshd_config (/etc/ssh/) by SSH

X11Forward yes

• old way - no need to follow

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

---

• Hypergraph: EC class

Windows

• MS-Word - 편집시 변경내용 추적