This page is under construction. Eric Martz 23:26, 11 December 2020 (UTC)
PACUPP is an open-source free program for identifying and visualizing cavities in macromolecules. It is a Jmol script that fills pockets, cavities, tunnels/channels in proteins with pseudoatoms. PACUPP provides tools to isolate cavities of interest and display their contents, their linings (and list the lining atoms, spreadsheet-ready), entrances (mouths), volumes, shapes, and dimensions.
PACUPP adds the pseudoatoms (holmium, Ho, think "holes") to an output PDB file, which can then be viewed in Jmol with PACUPP commands, or in the software of your choice (e.g. PyMOL, Chimera, VMD, Cn3D, etc.). PACUPP (Jmol) is Java-based, and thus works in Windows, macOS, and linux.
PACUPP Version 1.0 was released December 9, 2020.
The PACUPP program and documentation can be downloaded at molviz.org/pacupp. There you will also find a YouTube Video demonstrating how to use PACUPP with several examples, and a slideshow also providing examples and some guidance in how to use the program.
Example
At right is a (alpha-N-acetylgalactosaminidase) 2ixb[1]. It has a channel containing NAD, and a pocket where substrate can access the catalytic site, which includes the NAD.
With default settings (cavity detail: fine; cavity size: small), the two entrances to the channel containing NAD are not quite connected. With cavity detail set to very fine, the channel connects. having 5 or more pseudoatoms/cavity[2]. All but one of these are shallow pockets on the surface. In contrast, the pink cavity penetrates into the protein.
Color by depth and isolate
This is easier to see when the (PACUPP command d; also the backbone trace was toggled off with the command b). Only the formerly pink (largest) cavity has blue (deep) pseudoatoms. In PACUPP, .
Inside the cavity
, the NAD is visible near substrate (GalNAc). The PACUPP views command v evokes a menu offering this view.
