Uppsala Software Factory - VOIDOO Package
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- FLOOD to fill a cavity with water
- MAPROP to produce maps of various
- VOIDOO to find cavities and analyse
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an O macro that will generate and draw a solvent-accessible surface; uses
surface.csh and VOIDOO
an O macro that will generate and draw a van der Waals surface; uses
surface.csh and VOIDOO
script to merge multiple cavities found by VOIDOO into one map file
script to run VOIDOO to find cavities
script to run VOIDOO to generate the solvent-accessible surface;
mappage the surface with MAPMAN
- Tutorial: Visualisation of tunnels. This
explains how to visualise tunnels and other cavities in your
protein that are connected to the outside world. The tutorial
uses only Uppsala programs (MOLEMAN2, VOIDOO, MAMA, MAPMAN, and O).
VOIDOO is a program for detection of cavities
in macromolecular structures. It uses an algorithm that makes it
possible to detect even certain types of cavities that are connected
to "the outside world". Three different types of cavity can be handled
by VOIDOO: Vanderwaals cavities (the complement of the molecular
Vanderwaals surface), probe-accessible cavities (the cavity volume that
can be occupied by the centres of probe atoms) and MS-like probe-occupied
cavities (the volume that can be occupied by probe atoms, i.e.
including their radii).
VOIDOO can be used for:
- detecting and delineating cavities
- measuring cavity volumes and molecular volumes
- identifying non-protein atoms inside cavities
- identifying protein atoms that line the surface of cavities
- producing display files for O for visualising cavities
- producing macro files for O to display (1) non-protein
residues (ligands, solvent molecules) that are situated inside
each cavity, and (2) protein residues that surround each cavity
- producing display files for O for visualising molecular
- (randomly) rotating molecules for assessing the accuracy of cavity
volumes (by repeated calculations using differently oriented
copies of a molecule)
VOIDOO is available for SGI, DEC ALPHA, LINUX and OSX systems.
Visualisation of cavities and molecular surfaces requires O. Several
library files with Vanderwaals radii are provided, e.g. one with values
taken from AMBER, the other with values to emulate Connolly's MS program.
MAPROP comes with several precooked library files.
- GJ Kleywegt, JY Zou, M Kjeldgaard & TA Jones. International
Tables for Crystallography, Volume F. Chapter 17.1, pp. 353-356,
- GJ Kleywegt & TA Jones, Acta Cryst.,
D50, 178-185 (1994).
Latest update at 20 September, 2002.