Atoms Values Trasp

Description

Atoms are rendered with transparency dependent on the associated scalar value. On one side of the threshold value the atoms are rendered as hard spheres. On the other side their transparency depend on distance from the threshold value.

This module converts the molecule to an uniform volume in which sites occupied by atoms are represented as spheres of points. Each point has value corresponding to the associated scalar atom value. The resulting volume is then volume rendered by the standard AVS/Express volume_render module.

Input Ports

structure_in MoleculeType Molecular data.

Parameters

Sphere radius list From where the radius of the spheres used is taken.
Fixed radius
The sphere radius is equal for all and it is set using the Scale slider
Atom radius
The radius is the one defined in the selected info set for the atom type
VdW radius
The radius is the Van der Wals one defined in the selected info set for the atom type
Scale numeric field The scale of the spheres.
Resolution numeric field The side of each cell of the resulting volume.
Threshold solid list Defines on which side of the threshold the atoms are rendered as solid spheres.
Above
The atoms which value is above the threshold are rendered as solid spheres
Below
The atoms which value is below the threshold are rendered as solid spheres
Values mapping list From where the color of the solid spheres is taken.
Atom color
The color is the one defined in the selected info set for the atom type
Solid color
The atoms are colored by the color defined below
Gamma numeric field The exponent for non linear transparency. If greater than one makes the differences in transparency more visible. Remember that atoms with a value. The transparency depends on the distance of the associated value from the range threshold (increase with distance). A value of exactly one disables this enhancement and the transparency is a linear function of the distance from the threshold.
Reverse mapping toggle Reverse the mapping of values to transparency. If set atoms near the threshold are more transparent respect to the distant ones.
Use manual limits toggle The range for values is set in the fields below. If not set the value limits are computed by the module and show in the fields below.
Min numeric fields Lower value limit for the range.
Max numeric fields Upper value limit for the range.
Threshold slider Threshold value between the two value ranges (solid and semi transparent).
Solid color color chooser Select the solid sphere color.

Output Ports

obj DefaultObject The renderable version of the volume.
Return to index