A Python package for RNA Motif Library creation.
preprint: (insert paper link here)
All motifs are indentified as strings as mtype-msize-msequence-pdb_id. This is a unique format that may be visually unappealing but is easy to work with and is easy to parse.
mtype is the motif type (like HAIRPIN, HELIX, etc).
msize is the motif size (like 1, 2, 3, etc).
msequence is the motif sequence (like A, C, G, U, etc).
pdb_id is the PDB ID (like 1GID, 1GID, etc).
All residues are indentified as strings as chain_id-res_id-res_num-ins_code. This is a unique format that may be visually unappealing but is easy to work with and is easy to parse. These will all match the CIF files downloaded from the PDB.
chain_id is the chain identifier (auth_asym_id in CIF format).
res_id is the residue identifier (auth_comp_id in CIF format).
res_num is the residue number (auth_seq_id in CIF format).
ins_code is the insertion code (pdbx_PDB_ins_code in CIF format), most of the time this is empty.
Although trival to parse there is a function in util.py named parse_residue_identifier that can be used to parse the residue identifier into a dictionary.
# STEP 1: Get the latest RNA 3D Hub release
python rna_motif_library/setup_database.py get-atlas-release
# STEP 2: Generate a list of RNA PDBs with resolution better than 3.5Å
python rna_motif_library/setup_database.py get-all-rna-pdbs
# STEP 3: Download the PDBs
python rna_motif_library/setup_database.py download-cifs data/csvs/rna_structures.csv
# STEP 4: Process the PDBs with DSSR
python rna_motif_library/setup_database.py generate-dssr-outputs data/csvs/rna_structures.csv
A default CSV (nrlist_3.262_3.5A.csv) is in the directory data/csvs.
Make sure to download the most recent data (3.5 Å resolution):
http://rna.bgsu.edu/rna3dhub/nrlist
In the directory data/csvs, delete the default CSV file and replace with your download.
# Clone the repository and navigate to project directory
git clone https://github.com/YesselmanLab/rna_motif_library.git
cd rna_motif_library
# Create and activate new conda environment
conda create --name rna_motif_env python=3.8
conda activate rna_motif_env
# Install the package
pip install .
# Make sure you put the downloaded CSV in the right place or you will get errors
# Put the CSV where the default CSV is and delete the default
# Note: despite the use of "PDB" in language, all files are actually ".cif", not ".pdb"
# ALWAYS CLEAR THE data/out_csvs DIRECTORY BEFORE RUNNING THE SCRIPT (if it exists)! Move the data somewhere else if you want to keep it.
# If this folder is not empty (its nonexistence is OK), there will be problems!
# To create the library first we need to download the PDBs specified in the CSV
python rna_motif_library/cli.py download-cifs --threads 8
# Replace "8" with the number of CPU cores you want to use
# Estimated time: 15 minutes for around 2000 .cifs
# Expect a progress bar when it's working
# After downloading we need to process with DSSR
# need DSSR installed which is not included here
python rna_motif_library/cli.py process-dssr --threads 8
# Replace "8" with the number of CPU cores you want to use
# There will be visual feedback in the terminal window if it's working properly
# Feedback will consist of the path to the PDB/CIF files
# After processing with DSSR we need to process with SNAP
python rna_motif_library/cli.py process-snap --threads 8
# Replace "8" with the number of CPU cores you want to use
# There will be visual feedback in the terminal window if it's working properly
# Feedback will consist of the path + other information on nucleotides/etc
# After processing with SNAP we need to generate motif files
python rna_motif_library/cli.py generate-motifs
# There will be visual feedback in the terminal window if it's working properly
# Feedback will display the names of the motifs being processed
# ligand stuff
python rna_motif_library/ligand.py find-all-potential-ligands
python rna_motif_library/ligand.py get-ligand-cifs
python rna_motif_library/ligand.py get-hbond-donors-and-acceptors
python rna_motif_library/ligand.py get-ligand-info
python rna_motif_library/ligand.py get-ligand-polymer-instances