Command Line

Open the terminal, command prompt or PowerShell and navigate to the ProPores2 folder with the propores (or propores.exe) executable. The general command setup on Windows is

propores.exe <run command(s)> -i <path> -o <path> [options...]

and on MacOS or Linux:

./propores <run command(s)> -i <path> -o <path> [options...]

The three run commands are pore-id, axis-trace and gate-open, and at least one of them has to be given. The input protein PDB file -i and the output directory -o are always required. A full list of available parameters and options can be found here, or can be obtained on the command line by running propores.exe -h or propores.exe --help. Some use case examples are listed below.

Example 1: Only Pore Identification

Running only pore identification with 0.5 Ångstrom resolution, with the option to run axis trace and gate opening at a later point.

propores.exe pore-id -i input/1EA5_R.pdb -o output --name example -b 0.5

This writes the pore identification output, as well as files for independent axis trace and gate opening, to the folder output/example/ in the ProPores2 folder.

Example 2: Only Axis Trace

Running only axis trace based on previously generated files. For a single pore:

propores.exe axis-trace -i input/1EA5_R.pdb -o output --name example -ts output/example/axis_trace_input/0_pore.tsv

and for all pores in a directory:

propores.exe axis-trace -i input/1EA5_R.pdb -o output --name example -td output/example/axis_trace_input

This writes the axes to the folder output/example/axes.

Example 3: Only Gate Opening

Running only opening based on previously generated files. For a single pore:

propores.exe gate-open -i input/1EA5_R.pdb -o output --name example -gs output/example/gate_open_input/0_pore.tsv

and for all pores in a directory:

propores.exe gate-open -i input/1EA5_R.pdb -o output --name example -gd output/example/gate_open_input

While most gates can be opened within seconds, some gates have a very large number of possible residue configurations and can therefore take a lot longer. ProPores2 estimates the difficulty of each gate based on the residue composition, and gates can be skipped based on that difficulty:

propores.exe gate-open -i input/1EA5_R.pdb -o output --name example -gd output/example/gate_open_input --difficulty 1

This writes the protein versions with open gates to the folder output/example/gate_open.

Example 4: Everything at Once

propores.exe pore-id axis-trace gate-open -i input/1EA5_R.pdb -o output --name example -b 0.5 --difficulty 1