Compute SE Surface

Description

Compute the molecule Solvent Excluded Surface using the MSMS (Molecular Surface Computation Home Page - Michel F. Sanner) tool.

Input Ports

molecule_in MolecularDataType Molecule.

Parameters

Probe radius float The radius of the probe used to find the solvent excluded surface (normally 1.4).
Triangulation density float The triangle density of the resulting surface. Bigger number means better quality, but over 6 there is no improvement.
Surface coloring radio buttons Set the value used to color the surface. Possible values are:
no color
The surface has the default color set by Editors->Object->Properties->Primary Color.
color by nearest atom type
Every node is colored by the type of the nearest atom. The color is the same used by the ball-and-stock molecule representation.
color by charge
Every node is colored by the nearest atom charge.
color by atomic number
Every node is colored by the nearest atom atomic number.
Surface opacity slider The surface opacity value.
Surface rendering type radio buttons The surface can be rendered as a surface, as wireframe or as points.

Output Ports

fld Field The surface.
obj DefaultObject The renderable version of fld.

Interface to MSMS executable

This module uses an external executable to compute the Solvent Excluded Surface. The executables for Linux and Windows are distributed with STM3 in the directory msms. The path to the executable is defined in the avsenv file and it is called MSMSSERVER.

The executable creates some temporary file under the first directory available in this list:

The temporary files are called: stm3msmsXXXXXX where XXXXXX is some number.

See also