Quickstart Guide

Run fpocketR from the command line to analyze RNA structures and visualize ligand binding pockets.

Activate the fpocketR Environment

conda activate fpocketR

Tip: For a full list of options, run:

python -m fpocketR --help

Basic Structure Analysis

Analyze a local PDB file or fetch by PDB ID using the -pdb argument:

python -m fpocketR -pdb 3e5c.pdb
# or
python -m fpocketR -pdb 3e5c

Outputs pockets in tertiary structure:

Pocket color legend:

Secondary Structure Visualization

Add a secondary structure diagram using the -ss argument:

python -m fpocketR -pdb 2l1v.pdb -ss 2l1v.nsd

Outputs pockets in secondary structure:

Multistate Analysis

Analyze all NMR or Cryo-EM states using the --state 0 argument:

python -m fpocketR -pdb 2l1v.pdb -ss 2l1v.nsd --state 0

Outputs pocket density in 3D and 2D:

Apo/Holo Analysis

Align ligand-bound (holo) and ligand-free (apo) structures for direct comparison using the --alignligand argument:

python -m fpocketR -pdb 8f4o_apo.pdb --alignligand 2gdi_holo.pdb --knownnt 19,20,42,43

Outputs apo structure and aligned apo/holo structures:

Additional Arguments

Customize analysis with optional arguments:

• Select RNA chain: -c (--chain)

• Select ligand: -l (--ligand)

• Set raytracing resolution (lower = faster): -dpi (--dpi)

• Specify output path: -o (--out)

python -m fpocketR -pdb 2gdi_holo.pdb --chain Y --ligand TPP --dpi 10 --out ./TPP_RS

• Output files and figures add to custom directory: ./TPP_RS/2gdi_holo_clean_out/.

Outputs low resolution (fast) tertiary structure: