From CSBLwiki
Environment Setup
- 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
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
source ~/.cshrc
- 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 &
Methods
