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Copy pathStep3_Phenix&Phaser_Commands.sh
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Step3_Phenix&Phaser_Commands.sh
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source /opt/phenix-1.12-2829/phenix_env.sh #change accordingly if the version on the computer used is different
source /opt/ccp4/ccp4-7.0/bin/ccp4.setup-sh
#Comannds to run Phenix refine module
phenix.refine /mnt/auto/data_diectory/MFP013_03-13_MRmodelEdit_Ver3.pdb \
input.sequence.file_name="/mnt/auto/data_diectory/MFP013.fasta" \
input.xray_data.labels='/mnt/auto/data_diectory/MFP013IADPsoaking_02-04_2LoopsMonomerMR_2nmol.mtz:F(+),SIGF(+),F(-),SIGF(-),merge' \
xray_data.force_anomalous_flag_to_be_equal_to=true \
refinement.input.xray_data.convert_to_non_anomalous_if_ratio_pairs_lone_less_than_threshold=0.2 \
output.serial=1 \
output.prefix=IADP013_02-04_RefineInitRun01 \
xray_data.r_free_flags.generate=true \
xray_data.r_free_flags.fraction=0.05 \
xray_data.r_free_flags.disable_suitability_test=false \
refinement.main.number_of_macro_cycles=2 nproc=6 \
optimize_mask=true \
write_eff_file=true write_geo_file=true write_model_cif_file=true \
write_def_file=true write_maps=false write_map_coefficients=true \
anom_map_type=llg \
refinement.refine.strategy=individual_sites+individual_sites_real_space+individual_adp+occupancies+tls \
adp.individual.anisotropic="not water and not element H" \
optimize_xyz_weight=true optimize_adp_weight=true \
ordered_solvent=false ordered_solvent.mode=second_half \
refinement.ordered_solvent.output_chain_id=D \
simulated_annealing=false simulated_annealing.mode=first \
simulated_annealing.start_temperature=4000 \
# More commands for set up parameters
#/mnt/auto/data_diectory/AllFrame_IADP013_002-04_free.mtz \ #optional commands for references
#/mnt/auto/data_diectory/group_se_1.params \ #optional commands for more parameters
#xray_data.force_anomalous_flag_to_be_equal_to=true \
#anomalous_scatterers.group.selection="element SE" \
#anomalous_scatterers.group.f_prime=-24.99 \
#anomalous_scatterers.group.f_double_prime=7.99 \
#anomalous_scatterers.group.refine=f_prime+f_double_prime \
#wxc_scale=5 wxu_scale=10 \
#Commands to run Phenix phaser module on HPC, with a For loop function
module load ccp4/7.0 xds/2019 phenix/1.14-3260
source phenix_env.sh
source /hpcf/authorized_apps/rhel7_apps/ccp4/ccp4-7.0/bin/ccp4.setup-sh #the HPC package setup/version
for i in 006-003 006-009 006-013 006-001
do
cd "/research/home/data_directory/$i"
pwd
phenix.phaser HKLI /research/home/data_directory/$i/DataFiles/AUTOMATIC_DEFAULT_free.mtz \
ENSE Jak2JH1 PDB /research/home/data_directory/Jak2JH1SearchEnsemble.pdb \
IDEN 0.9 COMP PROT SEQ /research/home/data_directory/MFP053.fasta \
NUM 1 SEAR ENSE Jak2JH1 NUM 1 \
SPAC P3121 SGAL ALL \
ROOT Ruxo$i-EnseSearch \
done
#Commands to run CCP4 Matthew Coefficient and Phaser
matthews_coef << eof
CELL 110.22 110.22 60.61
SYMM 78
MOLW 16992.0
AUTO
RESO 3
XMLO
eof
Nmol/asym Matthews Coeff %solvent P(1.90) P(tot)
_____________________________________________________________
1 7.04 82.54 0.00 0.00
2 3.52 65.07 0.05 0.10
3 2.35 47.61 0.91 0.87
4 1.76 30.14 0.03 0.02
5 1.41 12.68 0.00 0.00
_____________________________________________________________
phaser << eof
TITL MFP022_010-07_3LoopsDimerMR_2nmol
MODE MR_AUTO
HKLI /mnt/auto/data_directory/Trunc251-521F_P43_MFP022_010-07_free.mtz
ENSE hHSP90aCTD PDB /mnt/auto/data_directory/hsHSP90a_CTDDimer_3LoopsTrunc_3q6m.pdb IDEN 95
SEAR ENSE hHSP90aCTD NUM 2
COMP PROT SEQ /mnt/auto/data_directory/MFP022.fasta NUM 4
ROOT MFP022_010-07_3LoopsDimerMR_2nmol
SELECT TEST ALL
MUTE OFF
VERBOSE ON EXTRA
SCRIPT ON
eof
phaser -xml 013I_002-04_phaser
MODE MR_AUTO
HKLI /mnt/auto/data_directory/AllFrame_IADP013_002-04_free.mtz
ENSE hTRAP1CTD PDB /mnt/auto/data_directory/hsTRAP1CTD_Echain_MRmodel_trunc01.pdb IDEN 90
ENSE hTRAP1CTD PDB /mnt/auto/data_directory/hsTRAP1CTD_Echain_MRmodel_trunc02.pdb IDEN 90
COMP PROT SEQ /mnt/auto/data_directory/MFP013.fasta NUM 2
SEAR ENSE hTRAP1CTD NUM 2
ROOT IADP013_002-04_AllFrame
SPAC 92
SELECT TEST ALL
MUTE OFF
VERBOSE ON EXTRA
SCRIPT ON
START