X-ray programs
From CSBLwiki
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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> | ||
+ | phenix.autosol peak_scala1.mtz seq_file=sde2656.fas wavelength_name=peak atom_type=Se lambda=0.97942 sites=14 peak.labels='F_New(+) SIGF_New(+) F_New(-) SIGF_New(-)' run_command="qsub -q infi" background=False nproc=4 nbatch=4 > & sol.0 & | ||
</pre> | </pre> | ||
== Methods == | == Methods == | ||
*[[Molecular replacement]] | *[[Molecular replacement]] |
Latest revision as of 06:44, 29 May 2011
Contents |
Environment Setup
panflam
- this tutorial is based on tcsh login shell
- CCP4 current release 1.6.2 (add a line into your .cshrc)
source /home/x-ray/setup-scripts/csh/ccp4.setup source /home/x-ray/setup-scripts/csh/ccp4-others.setup
- CNS_solve: current version 1.2 (Oct. 2009)
source /home/x-ray/cns_solve_1.2/cns_solve.env
source /home/x-ray/phenix-1.5-2/phenix_env
- 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
- installed programs & setup (modify your .cshrc)
# 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 &
phenix.autosol peak_scala1.mtz seq_file=sde2656.fas wavelength_name=peak atom_type=Se lambda=0.97942 sites=14 peak.labels='F_New(+) SIGF_New(+) F_New(-) SIGF_New(-)' run_command="qsub -q infi" background=False nproc=4 nbatch=4 > & sol.0 &