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autodrrafter_commands.txt
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# auto-DRRAFTER and ERRASER2 modeling
##############################################################################
##############################################################################
# Inputs
# General
# higest threshold that all connection seen
# generally select bottom of SL5b stem as point
##############################################################################
##############################################################################
##############################################################################
# SARS CoV 2 SL5
##############################################################################
map=../Coronavirus_SL5/maps/SARS_CoV_2-4p74-cryosparc_P1_J842_map_sharp.mrc
resolution=4.74
fasta=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL5.fasta
threshold=0.3
end_node=8
# SARS CoV 2 SL5 m2seq_librarySHAPE_eternafold
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL5_m2seq_librarySHAPE_eternafold.secstruct
out=SARS_CoV_2-SL5_m2seq_librarySHAPE_eternafold
# SARS CoV 2 SL5 sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL5_Sun_icSHAPE.secstruct
out=SARS_CoV_2-SL5_Sun_icSHAPE
# SARS CoV 2 SL5 library DMS
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL5_libraryDMS.secstruct
out=SARS_CoV_2-SL5_libraryDMS
##############################################################################
# SARS CoV 1 SL5
##############################################################################
map=../Coronavirus_SL5/maps/SARS_CoV_1-7p05-cryosparc_P18_J109_map_sharp.mrc
resolution=7.05
fasta=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_1.fasta
threshold=0.1
end_node=15
# SARS CoV 1 SL5 eternafold
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_1_eternafold.secstruct
out=SARS_CoV_1_eternafold
# SARS CoV 1 SL5 sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_1_Sun_icSHAPE.secstruct
out=SARS_CoV_1_Sun_icSHAPE
##############################################################################
# MERS SL5 con 1
##############################################################################
fasta=../Coronavirus_SL5/models/modeling_inputs/MERS.fasta
# con 1
map=../Coronavirus_SL5/maps/MERS_con1-6p89-cryosparc_P1_J318_map_sharp.mrc
resolution=6.89
threshold=0.24
end_node=5
# con 2
map=../Coronavirus_SL5/maps/MERS_con2-6p37-cryosparc_P1_J320_map_sharp.mrc
resolution=6.37
threshold=0.23
end_node=10
# con 3
map=../Coronavirus_SL5/maps/MERS_con3-6p44-cryosparc_P1_J323_map_sharp.mrc
resolution=6.44
threshold=0.25
end_node=14
# MERS sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/MERS_Sun_icSHAPE.secstruct
out=MERS_Sun_icSHAPE
# MERS DMS
secstruct=../Coronavirus_SL5/models/modeling_inputs/MERS_DMS.secstruct
out=MERS_DMS
# MERS SHAPE
secstruct=../Coronavirus_SL5/models/modeling_inputs/MERS_SHAPE.secstruct
out=MERS_SHAPE
##############################################################################
# BtCoV HKU5 SL5
##############################################################################
fasta=../Coronavirus_SL5/models/modeling_inputs/BtCoV_HKU5.fasta
# con 1
map=../Coronavirus_SL5/maps/BtCoV_HKU5_con1-5p93-cryosparc_P2_J362_map_sharp.mrc
resolution=5.93
threshold=0.18
end_node=12
# con 2
map=../Coronavirus_SL5/maps/BtCoV_HKU5_con2-6p42-cryosparc_P2_J365_map_sharp.mrc
resolution=6.42
threshold=0.165
end_node=8
# con 3
map=../Coronavirus_SL5/maps/BtCoV_HKU5_con3-8p00-cryosparc_P2_J368_map_sharp.mrc
resolution=8.00
threshold=0.16
end_node=17
# con 4
map=../Coronavirus_SL5/maps/BtCoV_HKU5_con4-7p29-cryosparc_P2_J371_map_sharp.mrc
resolution=7.29
threshold=0.19
end_node=10
# BtoCoV sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/BtCoV_HKU5_Sun_icSHAPE_G317A.secstruct
out=BtCoV_HKU5_Sun_icSHAPE_G317A
# BtoCoV dms
secstruct=../Coronavirus_SL5/models/modeling_inputs/BtCoV_HKU5_dms.secstruct
out=BtCoV_HKU5_dms
# BtoCoV shape
secstruct=../Coronavirus_SL5/models/modeling_inputs/BtCoV_HKU5_shape.secstruct
out=BtCoV_HKU5_shape
# BtoCoV eternafold
secstruct=../Coronavirus_SL5/models/modeling_inputs/BtCoV_HKU5_eternafold.secstruct
out=BtCoV_HKU5_eternafold
#######################################
# HCoV NL63 SL5
#######################################
fasta=../Coronavirus_SL5/models/modeling_inputs/HCoV_NL63.fasta
# con 1
map=../Coronavirus_SL5/maps/HCoV_NL63_con1-8p42-cryosparc_P3_J1258_map_sharp.mrc
resolution=8.42
threshold=0.3
end_node=7
# con 2
map=../Coronavirus_SL5/maps/HCoV_NL63_con2-8p95-cryosparc_P3_J1250_map_sharp.mrc
resolution=8.95
threshold=0.3
end_node=7
# NL63 sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/HCoV_NL63_Sun_icSHAPE.secstruct
out=HCoV_NL63_Sun_icSHAPE
# NL63 eterna
secstruct=../Coronavirus_SL5/models/modeling_inputs/HCoV_NL63_eternafold.secstruct
out=HCoV_NL63_eternafold
##############################################################################
# HCoV-229E - SL5
##############################################################################
fasta=../Coronavirus_SL5/models/modeling_inputs/HCoV_229E.fasta
map=../Coronavirus_SL5/maps/HCoV_229E-6p48-cryosparc_P3_J880_map_sharp.mrc
resolution=6.48
threshold=0.65
end_node=7
end_node=1
# 229E eterna
secstruct=../Coronavirus_SL5/models/modeling_inputs/HCoV_229E_eternafold.secstruct
out=HCoV_229E_eternafold
# 229E react
secstruct=../Coronavirus_SL5/models/modeling_inputs/HCoV_229E_react.secstruct
out=HCoV_229E_react
# 229E manual
secstruct=../Coronavirus_SL5/models/modeling_inputs/HCoV_229E_manual.secstruct
out=HCoV_229E_manual
# 229E rnastructure
secstruct=../Coronavirus_SL5/models/modeling_inputs/HCoV_229E_rnastructure.secstruct
out=HCoV_229E_rnastructure
##############################################################################
# SARS2 SL56 - SL5
##############################################################################
fasta=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_SL5only.fasta
map=../Coronavirus_SL5/maps/SARS_CoV_2_SL56-7p83-flipped-cryosparc_P3_J1413_map_sharp.mrc
resolution=7.83
threshold=0.5
end_node=8
# SL56-5only eternafold
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_SL5only_eternafold.secstruct
out=SARS_CoV_2-SL56_SL5only_eternafold
# SL56-5only m2seq
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_SL5only_m2seq.secstruct
out=SARS_CoV_2-SL56_SL5only_m2seq
# SL56-5only sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_SL5only_Sun_icSHAPE.secstruct
out=SARS_CoV_2-SL56_SL5only_Sun_icSHAPE
##############################################################################
# SARS2 SL56 5bext - SL5
##############################################################################
fasta=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5bext_SL5only.fasta
map=../Coronavirus_SL5/maps/SARS_CoV_2_SL56_5bext-7p40-flipped-cryosparc_P3_J1278_map_sharp.mrc
resolution=7.40
threshold=0.28
end_node=17
# SL56-5bext-5only eternafold
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5bext_SL5only_eternafold.secstruct
out=SARS_CoV_2-SL56_5bext_SL5only_eternafold
# SL56-5bext-5only m2seq
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5bext_SL5only_m2seq.secstruct
out=SARS_CoV_2-SL56_5bext_SL5only_m2seq
# SL56-5bext-5only sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5bext_SL5only_Sun_icSHAPE.secstruct
out=SARS_CoV_2-SL56_5bext_SL5only_Sun_icSHAPE
##############################################################################
# SARS2 SL56 5cext - SL5
##############################################################################
fasta=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5cext_SL5only.fasta
map=../Coronavirus_SL5/maps/SARS_CoV_2_SL56_5cext-9p07-cryosparc_P3_J1247_map_sharp.mrc
resolution=9.07
threshold=1.05
end_node=5
# SL56-5cext-5only eternafold
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5cext_SL5only_eternafold.secstruct
out=SARS_CoV_2-SL56_5cext_SL5only_eternafold
# SL56-5cext-5only m2seq
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5cext_SL5only_m2seq.secstruct
out=SARS_CoV_2-SL56_5cext_SL5only_m2seq
# SL56-5cext-5only sun
secstruct=../Coronavirus_SL5/models/modeling_inputs/SARS_CoV_2-SL56_5cext_SL5only_Sun_icSHAPE.secstruct
out=SARS_CoV_2-SL56_5cext_SL5only_Sun_icSHAPE
##############################################################################
##############################################################################
# Running auto-DRRAFTER
##############################################################################
##############################################################################
nstruct_per_job=100
ncycles=30000
rosetta_dir=$ROSETTA/main/source/bin/
rosetta_ext=.default.linuxgccrelease
njobs=50
ncycles=30000
ml biology eman2
# SETUP
python $ROSETTA/main/source/src/apps/public/DRRAFTER/auto-DRRAFTER_setup.py \
-map_thr $threshold \
-full_dens_map $map \
-full_dens_map_reso $resolution \
-fasta $fasta \
-secstruct $secstruct \
-out_pref $out \
-rosetta_directory $rosetta_dir \
-nstruct_per_job $nstruct_per_job \
-cycles $ncycles \
-fit_only_one_helix \
-rosetta_extension $rosetta_ext \
-use_end_node $end_node \
# SUBMIT
round=R1
python $ROSETTA/main/source/src/apps/public/DRRAFTER/submit_jobs.py \
-out_pref $out \
-curr_round $round \
-njobs $njobs \
-template_submission_script job_submission_template.sh \
-queue_command sbatch
# ASSESS
round=FINAL_R4
python $ROSETTA/main/source/src/apps/public/DRRAFTER/auto-DRRAFTER_setup_next_round.py \
-out_pref $out \
-curr_round $round \
-rosetta_directory $rosetta_dir \
-rosetta_extension $rosetta_ext \
-nmodels 5000 \
-dens_thr $threshold \
# FINALIZE
round=FINAL_R4
python $ROSETTA/main/source/src/apps/public/DRRAFTER/finalize_models.py \
-fasta $fasta \
-out_pref $out \
-final_round $round
##############################################################################
##############################################################################
# Running ERRASER2
##############################################################################
##############################################################################
erraser2.default.linuxgccrelease -s *pdb -edensity:mapfile $map -edensity::mapreso $resolution -score:weights stepwise/rna/rna_res_level_energy7beta.wts -set_weights elec_dens_fast 10.0 cart_bonded 5.0 linear_chainbreak 10.0 chainbreak 10.0 fa_rep 1.5 fa_intra_rep 0.5 rna_torsion 10 suiteness_bonus 5 rna_sugar_close 10 -rmsd_screen 3.0 -mute core.scoring.CartesianBondedEnergy core.scoring.electron_density.xray_scattering -rounds 3 -fasta $fasta -cryoem_scatterers