Package: tem-simulator-scripts
tem-simulator-scriptsThis repository contains convenient scripts for the TEM-Simulator V1.3 (http://tem-simulator.sourceforge.net/)Installationconda create -n temscripts -c conda-forge python=3.9 biotite
conda activate temscripts
pip install tem-simulator-scriptsMake also sure that IMOD is installed, as thetsimscripts_pipe.shneeds the commandssubmfgandtrimvolfrom IMOD.PreparationDownload all PDBs you want to simulate. In case PDB is not available (only PDBx or mmcif), download
PDBX or mmcif and convert it to PDB withhttps://mmcif.pdbj.org/converter/index.php?l=en. Its recommended to download
directely the biological assemblies.OverviewHere we give a short overview of the scripts contained in this package:tsimscripts_pipe.sh: This is probably the only script a user needs from this collection.tsimscripts_gen_coords.py: Generates coordinates for particles that are not overlapping.tsimscripts_gen_input.py: This script generates the input file for the TEM-Simulator.tsimscripts_gen_filaments.py: Generate simulated filaments.tsimscripts_gen_raw_tilt.py: Generates the raw tilt file for IMOD.tsimscripts_gen_trans_file.py: Some PDBs needs transformation files. Simply use assemblies to avoid this script.tsimscripts_gen_map.py: Script to generates vesicle or fiducial maps.tsimscripts_extract.py: Extracts subvolumes of the simulated tomogram.Pipeline all commandsA convenient script is fully automating the whole process incl. reconstruction.It requires that imod is installed. The require files for simulating filaments can be found inresources/filament_filesA sample command looks like this:tsimscripts_pipe.sh--pdbspdbs/*.pdb--npdbs150--outputout_sim_tomo_1--random_seed10--pdbs_filfilament_files/*.pdb--settings_filfilament_files/*.json--nsubs100--random_seed10It will generate a tomogram with all pdbs included in the folderpdbs/and will add 4 vesicles and 10 fiducials.How to simulate a tomogram with particles from a single PDBYou can also run each step individually in case you want to have more control:Install the package with python setup.py installOptional: Generate trans files usingtsimscripts_gen_trans_file.py. Not necessary when using biological assemblies directly.Optional: Generate fiducial usingtsimscripts_gen_map.py: I would add 8-10 fiduicals. Patch tracking didnt work well.Generate coordinatetsimscripts_gen_coords.pyGenerate input file usingtsimscripts_gen_input_file.pyGenerate raw tilt file withtsimscripts_gen_raw_tilt.pyRunTEM-simulator input.txtReconstruction with etomoDuringCoarse AlignementI needed to use alow freq. rolloff sigmaof0.01, ahigh freq. cutoff sigmaof0.25and ahigh freq. rolloff sigmaof0.05. Moreover I activated the optionNo Cosine Stretch.InFinal Aligned Stack CompleteI set the binning to2InTomogram Generation In ProgressI set the thethickness in Zto300Extract the subvolumes withtsimscripts_extract.py: If you have used fiducials, check if they are centered in the extracted tomograms.
If they offcentered, repeat the alignement in step 7.How to simulate a tomogram with particles from multiple PDBsHere is a complete example how to simulate a tomogram. It assumes that there are several pdbs in the folder pdbs/.
Only the PDB 6x9q needed a trans_file in this example.tsimscripts_gen_map.pyfiducial-d50--apix1-v10000mkdirtrans_files
tsimscripts_gen_trans_file.pypdbs/6x9q.pdb
mv6x9q_trans.txttrans_files/
tsimscripts_gen_coords.py--pdbspdbs/*.pdb--npdbs20-ocoords/
tsimscripts_gen_input.py--pdbspdbs/*.pdbfiducial.mrc--transtrans_files/6x9q_trans.txt--coordscoords/*.txt--defocus_upper6--defocus_lower7TEM-simulatorinput.txt