Usage: Basic commands

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Victoria edited this page Apr 14, 2023 · 8 revisions

makestructuraldb: Creates a protein structure database which automatically computes protein-protein, protein-ligand and protein-nucleic interfaces if any.

makestructuraldb -pdb /path/to/pdb/file.pdb --blast_db /path/to/target_proteomeDB

makevariantsdb: Splits a file containing protein variants/positions to enable efficient mapping onto 3D structures afterwards.

makevariantsdb -vf /path/to/variants/file

mapper: Maps variants/protein positions to the structure of proteins, including their interfaces.

mapper -pid protein *or* transcript *or* gene *or* variantID -psdb /path/to/structuralDB -vdb /path/to/variantDB/ -ids idmapping_file.txt -csv

makevisualization: Generate ChimeraX scripts (.cxc) to visualize the mapping results.

makevisualization -p PDB_code -i InterfacePositions.csv -o output/folder/ -n script_base_name

The complete list of input arguments for each of the commands is available when typing -h.