BioEM Toolkit is a collection of tools that assist the run of BioEM on large experimental and synthetic datasets. This toolkit takes in a processed particle stack and a set of molecular models and runs the bioEM algorithm to determine the posterior probability that a given molecular model corresponds to a given particle image.
BioEM is run in two rounds. Round 1 is a simple uniform sampling to determine the angles in 3D space. Typically we search through 300 orientations in round 1 for each model and each particle. Round 2 is a more comprehensive search. We extract the best orientations calculated from each model in round 1 and compare them to generate a better estimate for the orientation. With the posterior probabilities calculated by bioEM, one can move on to estimate the free energy landscape captured by the particle stack using cryoBIFE and cryoRE.
For more information, see the bioEM documentation https://bioem.readthedocs.io/en/latest/.
git clone [email protected]:phu91/bioem_toolkit.gitBioEM Installation
Visit Visit https://github.com/bio-phys/BioEM for installation instruction
git clone [email protected]:bio-phys/BioEM.gitA conda environment is suggested to be setup before running the toolkit
conda env create -f environment.ymldisBatch is also required to launch ROUND 2
git clone [email protected]:flatironinstitute/disBatch.gitParticles must be in a stacked MRCS format for ROUND 1. Individual MRC file for each particles are required for ROUND 2. The naming scheme should be particle_
Individual particles (particle_0.mrc, particle_1.mrc, etc.) should be stored in a sub-group directory, such as particless/0-5k (from particle 0 to particle 5000), and the stacked MRCS particles_0-5k.mrcs should be stored in particles/.
In tools/prep_particles.py, you can execute this Python script to extract stacked or individual particles.
python prep_particles.py [-h] [--input INPUT] [--opath OPATH] [--output OUTPUT] [--start START] [--end END] [--method METHOD]Models must be in TXT format.
tools/prep_models_step1.tcl is a TCL script that works in VMD to extract the PDB. Assumed VMD is installed. Remember to adjust the I/O accordingly to your PDB and TRAJECTORY.
vmd -e prep_models_step1.tclAfter extracting PDB files, run this script in tools/prep_models_step1.sh to convert PDB to TXT format. Notes: The charges and electrons are fixed to default values.
./prep_models_step2.shALWAYS CHECK the parameter files in library/parameters such as Param_BioEM_template or any slurm submission scripts before running bioem_toolkit.
MODEL_LIST and GROUP_LIST can be found in the test/. BioEM is very delicate and serious about file handling, PLEASE DO NOT CHANGE anything if you are not sure about its functions because these small changes (etc., names) can cause BioEM to haul.
run_dry provides the running command to activate the interactive mode of the BioEM toolkit for FIRST TIME users. A command-line mode is activated with the flag -cmd. Notes: It is recommended to use a full (absolute) path format.
A template for MODEL_LIST and GROUP_LIST can be found in test/.
To run the bioem_toolkit, one would simply execute the run_dry file. Make sure that you change all the paths accordingly to your machine:
./run_dry-mp: Absolute path to where models are stored.
-ml: Text file with a list of all models.
-gl: List of groups which particles are organised into. Eg. 0-10k 0-10k.mrcs 10000
-param: Absolute path to parameters files which this script uses. Usually stored in the github repo in 'bioem_toolkit/library/parameters'.
-pp: Absolute path of directory where particle .mrcs files are stored.
-op: Directory where output will be stored.
python bioem_toolkit/bioem_toolkit.py -hPull requests are welcome. For significant changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.