AtomicSurf

DESCRIPTION

This module implements the QCPE (Quantum Chemistry Program Exchange #544) program USURF. This is a fast version of Connolly dot surface generation. It takes as input a pyramid-based molecule and produces a list of points in three space of the solvent accessible surface. This surface is calculated by rolling a probe atom over the molecule. Points on the molecule which are accessible by the probe are saved in the output lattice.

Typically, the output lattice should be wired to LatToGeom and then that output to the Render module.

INPUTS

Port: Molecule
Type: Pyramid
Constraints: n-layer
Constraints: optional-baseLat
Constraints: n-D compression
Constraints: n-compression type
The source Molecule pyramid.

WIDGETS

Port: Density
Type: Dial
A good dot density for proteins is 10.0.

Port: Probe Radius
Type: Slider
Atomic radius of probe atom. A radius of 1.5 corresponds to a water molecule. The larger the probe radius the coarser the detail of the surface. The smaller the probe radius the finer the surface detail.

OUTPUTS

Port: Dots
Type: Lattice
Constraints: 1-D
Constraints: long
Constraints: curvilinear
Constraints: 3-cD
The dot lattice. The data portion is the atom number associated with the dot located at the xyz coordinate.

KNOWN PROBLEMS

Limited currently to 8,000 atoms and 100,000 dots.

SEE ALSO

ReadPDB, BallStick.
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© The Numerical Algorithms Group Ltd, Oxford UK. 2000