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Fix infinite loop and empty filament option #3

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Fix infinite loop and empty filament option #3

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46 changes: 32 additions & 14 deletions pipeline/tsimscripts_pipe.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,7 @@ do
--defocus_upper) defocus_upper=${2}; shift; shift;;
--thickness) thickness=${2}; shift; shift;;
--s1) early_abort=true; shift;;
*) echo "unknown option ${1}"; exit 1
esac
done
mkdir -p $(dirname ${output})
Expand Down Expand Up @@ -132,11 +133,7 @@ echo PDBS FIL: ${pdbs_fil[@]}
echo SETTINGS FIL: ${settings_fil[@]}
echo NSUBS: ${nsubs[@]}

echo $(date) - Generate filaments
cp ${pdbs[@]} ${particle_pdb_dir}
cp ${pdbs_fil[@]} ${filament_pdb_dir_in}
cp ${settings_fil[@]} ${filament_pdb_dir_in}
tsimscripts_gen_filaments.py --pdbs ${filament_pdb_dir_in}/*.pdb --settings ${filament_pdb_dir_in}/*.json --nsubs ${nsubs[@]} ${seed_cmd_3} -o ${filament_pdb_dir}

echo $(date) - Generate PDB to MRC input files
tsimscripts_gen_input.py particle --pdbs ${particle_pdb_dir}/*.pdb --output_file ${ptcls_dir}/input.txt
Expand All @@ -146,13 +143,23 @@ TEM-simulator input.txt
rm *_map_im.mrc
cd -

echo $(date) - Generate PDB to MRC input files filament
tsimscripts_gen_input.py particle --pdbs ${filament_pdb_dir}/*.pdb --output_file ${ptcls_fil_dir}/input.txt
cd ${ptcls_fil_dir}
echo $(date) - Run PDB to MRC filament
TEM-simulator input.txt
rm *_map_im.mrc
cd -
if [[ ${#pdbs_fil} -ne 0 ]]
then
echo $(date) - Generate filaments
cp ${pdbs_fil[@]} ${filament_pdb_dir_in}
cp ${settings_fil[@]} ${filament_pdb_dir_in}
tsimscripts_gen_filaments.py --pdbs ${filament_pdb_dir_in}/*.pdb --settings ${filament_pdb_dir_in}/*.json --nsubs ${nsubs[@]} ${seed_cmd_3} -o ${filament_pdb_dir}

echo $(date) - Generate PDB to MRC input files filament
tsimscripts_gen_input.py particle --pdbs ${filament_pdb_dir}/*.pdb --output_file ${ptcls_fil_dir}/input.txt
cd ${ptcls_fil_dir}
echo $(date) - Run PDB to MRC filament
TEM-simulator input.txt
rm *_map_im.mrc
cd -
else
echo $(date) - Skip generate filaments
fi

echo $(date) - Generate fiducial template
tsimscripts_gen_map.py fiducial -d ${fiducialsize} --apix 1 --value 10000 --output_file ${fiducial_dir}/fiducial.mrc
Expand All @@ -161,13 +168,24 @@ echo $(date) - Generate vesicle template
tsimscripts_gen_map.py vesicle -d ${vesiclesize} --apix 10 --value 2 --output_file ${fiducial_dir}/vesicle.mrc

echo $(date) - Generate coordinates
tsimscripts_gen_coords.py --pdbs ${filament_pdb_dir}/*.pdb --npdbs 3 --ptcls ${ptcls_fil_dir}/*.mrc ${seed_cmd_1} -o ${coords_fil_dir} --write_occupancy --write_raw_occupancy --tilt_range 15 --max_trials_pos 20 --max_trials_rot 20 --allow_clip --vheight ${thickness}
tsimscripts_gen_coords.py --pdbs ${particle_pdb_dir}/*.pdb --npdbs ${npdbs[@]} --maps ${fiducial_dir}/fiducial.mrc ${fiducial_dir}/vesicle.mrc --nmaps ${nfiducial} ${nvesicle} --ptcls ${ptcls_dir}/*.mrc ${seed_cmd_2} -o ${coords_dir} --write_occupancy --occupancy ${coords_fil_dir}/occupancy_raw.mrc --value_offset ${#pdbs_fil[@]} --vheight ${thickness}
if [[ ${#pdbs_fil} -ne 0 ]]
then
tsimscripts_gen_coords.py --pdbs ${filament_pdb_dir}/*.pdb --npdbs 3 --ptcls ${ptcls_fil_dir}/*.mrc ${seed_cmd_1} -o ${coords_fil_dir} --write_occupancy --write_raw_occupancy --tilt_range 15 --max_trials_pos 20 --max_trials_rot 20 --allow_clip --vheight ${thickness}
tsimscripts_gen_coords.py --pdbs ${particle_pdb_dir}/*.pdb --npdbs ${npdbs[@]} --maps ${fiducial_dir}/fiducial.mrc ${fiducial_dir}/vesicle.mrc --nmaps ${nfiducial} ${nvesicle} --ptcls ${ptcls_dir}/*.mrc ${seed_cmd_2} -o ${coords_dir} --write_occupancy --occupancy ${coords_fil_dir}/occupancy_raw.mrc --value_offset ${#pdbs_fil[@]} --vheight ${thickness}
else
tsimscripts_gen_coords.py --pdbs ${particle_pdb_dir}/*.pdb --npdbs ${npdbs[@]} --maps ${fiducial_dir}/fiducial.mrc ${fiducial_dir}/vesicle.mrc --nmaps ${nfiducial} ${nvesicle} --ptcls ${ptcls_dir}/*.mrc ${seed_cmd_2} -o ${coords_dir} --write_occupancy --vheight ${thickness}
fi


[[ ${early_abort} == true ]] && exit 0

echo $(date) - Generate 3D simulation input files
tsimscripts_gen_input.py tomogram --pdbs ${particle_pdb_dir}/*.pdb ${fiducial_dir}/fiducial.mrc ${fiducial_dir}/vesicle.mrc ${filament_pdb_dir}/*.pdb --coords ${coords_dir}/*.txt ${coords_fil_dir}/*.txt --defocus_upper ${defocus_upper} --defocus_lower ${defocus_lower} --output_file ${simulation_dir}/input.txt --thickness ${thickness}
if [[ ${#pdbs_fil} -ne 0 ]]
then
tsimscripts_gen_input.py tomogram --pdbs ${particle_pdb_dir}/*.pdb ${fiducial_dir}/fiducial.mrc ${fiducial_dir}/vesicle.mrc ${filament_pdb_dir}/*.pdb --coords ${coords_dir}/*.txt ${coords_fil_dir}/*.txt --defocus_upper ${defocus_upper} --defocus_lower ${defocus_lower} --output_file ${simulation_dir}/input.txt --thickness ${thickness}
else
tsimscripts_gen_input.py tomogram --pdbs ${particle_pdb_dir}/*.pdb ${fiducial_dir}/fiducial.mrc ${fiducial_dir}/vesicle.mrc --coords ${coords_dir}/*.txt --defocus_upper ${defocus_upper} --defocus_lower ${defocus_lower} --output_file ${simulation_dir}/input.txt --thickness ${thickness}
fi

cd ${simulation_dir}
echo $(date) - Run 3D simulation
Expand Down