Quick start
If you want to use Superpose3D right away without specifying a custom protein representation do the following:
1) Copy the files “query3d_par.txt” and “pdb_res_dict.txt” from the data/ subdir in the Superpose3D package into the directory where you put the superpose executable
2) Create an input file named input.txt with the following structure (everything is space NOT tab separated, if you are on windows use “/“ NOT “\” as directory separator)
pdb_dir PATH_TO_YOUR_PDB_DIRECTORY
probe PDB_FILE_CONTAINING_THE_PROBE_STRUCTURE(CHAIN)
target PDB_FILE_CONTAINING_THE_TARGET_STRUCTURE(CHAIN)
3) Launch Superpose3D using the query3d_par.txt parameters. Residues are described with two points: the C-alpha and the geometric centroid of the side chain residues. This is a good compromise between accuracy and speed and should be a good starting point for your analysis.
superpose -i input.txt -o out.txt -p query3d_par.txt
4) The output will be located in the file out.txt. Read the “Superimposing PDB files and visualising the structural similarities” section of the manual if you want to visualize the results with a molecular graphics software.