Outputs

Besides the descriptors CSV file described in Descriptors, Poké can write the files below. Each one is switched on by its own flag.

Extracted trajectory

Normally Poké does not produce a new trajectory. Use the -e flag to extract frames that contain at least one pocket into a new trajectory file (frames.xtc + structure.pdb).

Frames can be sorted by any pocket property using the -s flag (descending order). Combined with -n, only the top n frames are kept:

poke -dvp -e -s score -n 10 protein.pdb

The OutputFrame column in the descriptors CSV reflects the new frame ordering after sorting.

Volume points

The -v flag writes a multi-model PDB file (volumes.pdb) containing the grid points of each pocket. Each pocket is assigned a unique residue ID (starting at 800) with residue name PCK. The B-factor column stores the electrostatic potential value at each point.

Density maps

The -dx flag produces an OpenDX density map (density.dx) showing pocket occupancy across trajectory frames. The grid uses a 1.0 Å spacing with a 5.0 Å margin around the structure bounding box. If the mrcfile package is installed, an MRC format map (density.mrc) is also generated.

PyMOL script

The -p flag generates a PyMOL script (pymol.pml) that loads the structure, trajectory, and volume files and sets up a ready-to-use visualization.

Pickle

The -k flag saves the raw Pocket objects in a pickle file (pockets.pickle), one list per frame. This is useful for custom analysis in Python.

Histograms

The -g flag generates histogram plots (histograms/*.png) showing the distribution of each descriptor across all pockets found. The appearance can be customized with environment variables:

Variable	Description
`POKE_FONT`	Font family for plots
`POKE_FIGSIZE`	Figure size as comma-separated values (e.g., `8,4`)
`POKE_COLOR`	Override bar color
`POKE_QUANTILES`	Set to `no`, `false`, or `0` to hide quantile lines

Launch script

The -ls flag saves the full Poké command to a bash script (launch.sh) for reproducibility.

Compression

The -z flag compresses the volume PDB and pickle outputs using gzip (.pdb.gz, .pickle.gz). Most downstream programs can read gzip-compressed files directly.