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source /home/x-ray/ccp4/setup-scripts/csh/ccp4-others.setup | source /home/x-ray/ccp4/setup-scripts/csh/ccp4-others.setup | ||
</pre> | </pre> | ||
| - | + | *running ''phenix'' by 'qsub' on multiple processers [[panpyro]] | |
| - | + | *<b>EXAMPLE</b> | |
| + | <pre> | ||
# swissmodel superimposed to 1V19 MR solution | # 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.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 & | 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 & | ||
| - | <pre> | + | </pre> |
| - | + | ||
*[[X-ray programs]] | *[[X-ray programs]] | ||
*Methods | *Methods | ||
**[[Molecular replacement]] | **[[Molecular replacement]] | ||
| + | |||
| + | ==Computing resources== | ||
| + | #[[Compbio]] | ||
| + | #[[Microbio]] | ||
| + | #[[Panpyro]] | ||
| + | #[[Panflam]] | ||
| + | |||
| + | ==Unix & Programming== | ||
| + | ===Unix=== | ||
| + | *[https://help.ubuntu.com/community/InstallingCompilers Installing Compilers] | ||
| + | *[[SSH]] - how to connect the Lab. PC from your home | ||
| + | *X11 connection | ||
| + | **Easy safe way is to use SSH's X forwarding: | ||
| + | <pre>ssh -X me@remotemachine</pre> | ||
| + | *check ''ssh_config & sshd_config'' (/etc/ssh/) by [http://www.ssh.com/support/documentation/online/ssh/adminguide/32/X11_Forwarding.html SSH] | ||
| + | <pre>X11Forward yes</pre> | ||
| + | *<b>''old way - no need to follow''</b> | ||
| + | Your display will look to the remote machine like: | ||
| + | <pre>echo $DISPLAY | ||
| + | localhost:10.0 | ||
| + | firefox --display=$DISPLAY & | ||
| + | </pre> | ||
| + | ''xhost/export DISPLAY'' | ||
| + | *On your local machine: | ||
| + | <pre>xhost + remotemachine</pre> | ||
| + | *On the remote machine: | ||
| + | <pre>export DISPLAY=localhost:0.0</pre> | ||
| + | *After you're done, remove remote machine access from your xhost: | ||
| + | <pre>xhost -</pre> | ||
| + | |||
| + | *SCIM - [http://www.ubuntu.or.kr Input Hangul] | ||
| + | *Linux (Unix) [http://hancoma.springnote.com/pages/621424.xhtml commands] | ||
| + | *[http://tldp.org/ The Linux Document Projects] - Numerous useful documents & tutorials are available | ||
| + | *Change locale (language) for 'panpyro' | ||
| + | <pre>bash shell: | ||
| + | export LC_ALL=en_GB.ISO8859-1 | ||
| + | export LANG=en_GB.ISO8859-1 | ||
| + | </pre> | ||
| + | |||
| + | ===Python=== | ||
| + | *[http://openwetware.org/wiki/BE.180 BE.180 Biological Engineering Programming] - Synthetic biology@MIT Check "Unix&Python" tutorials! | ||
| + | **[[Media:python_sheet.pdf|Python Cheat Sheet]] | ||
| + | **[[Media:unxpython_tut_06.pdf|Unix&Python tutorial]] | ||
| + | |||
| + | ===Applications=== | ||
| + | *[[MySQL|MySQL]] | ||
| + | *[[Matlab|Matlab]] | ||
| + | *[[R|R-project]] | ||
| + | ---- | ||
| + | *[http://www.redbrick.dcu.ie/~noel/ECwheel.html Hypergraph: EC class] | ||
==Computing resources== | ==Computing resources== | ||
Revision as of 06:04, 8 November 2009
|
Protocols
Part list
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
Computing resources
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!
Applications
Computing resources
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!
Applications
Windows
- MS-Word - 편집시 변경내용 추적
