Visualize Bar

The visualize bar is divided into a few tabs:

  • Particles tab

    Controls the list of atoms / proteins / meshes.

  • Colors

    Controls the attributes and coloring of atoms.

  • Graphics

    Controls the options of realtime-rendering of the scene.

  • Render

    Controls the options of offline-rendering (image / video output).

  • Information

    Displays the math for the nerds, as well as additional information for selected atoms.

Particles Tab

The particles tab controls the drawing of atoms and proteins.

../../_images/vpart.png
Button Function
vexp Expands / Collapses the group
vsela Selects everything
vsel0 Deselects everything
vseli Flip selection
vbal Changes the draw mode (see Draw Modes) of the group / selection
veye Shows / Hides the group / selection

Atoms are grouped into Residues -> Residue ID -> atom name.

Todo

Add the protein section

Attributes Tab

Attributes

Attributes are general data for each particle, optionally animated. A system can have an arbitary number of attributes. Attributes can be filled with the Set Attribute node, and queried with the Get Attribute node.

../../_images/cattr.png

Colors

The colors section controls the color for atoms and bonds.

../../_images/cols.png ../../_images/grads.png
  • Bond colors
Option Details
Custom Bond Colors Use a custom color instead of atom colors
Blend Bond Colors Blend colors inherited from atoms

Radii

Option Details
Scale Multiply all radii values by this value

Bounding Box

Option Details
Draw Draw the Box in 3D view
Center X, Y, Z Box center coordinates
Periodic Wrap around atoms outside the bounding box

Orientation

  • Type
Type Details
Stretch Stretch atoms based on directions
Vector Draw per-atom arrows toward directions

Graphics Tab

The graphics tab controls the shading of the scene.

  • Shading
../../_images/gshd.png
Option Details
Classic The scene is shaded with Lambert and Blinn-Phong lighting. Slightly faster but lower quality.
PBR The scene is shaded with Environment Maps. Higher quality but slightly slower and uses more memory.
  • Lighting
../../_images/glight.png
Option Details
Sky Environment type (backgrounds are in the backgrounds/ folder)
Strength Strength of diffuse lighting (environment strength)
Falloff How much the light gets weaker when further away from the camera
Offset Falloff distance starts from this distance from the camera
Specular The strength of reflection. For PBR, diffuse intensity = 1 - specular intensity
Transparency Transparency ratio
IOR Index of Refraction for transparency
Background Background type: Color, Ambient, Sky
Color Background color
  • Camera
../../_images/gcam.png
Option Details
Follow Camera always centers on target
Center X,Y,Z Camera axis
Rotation W, Y Camera angle
Scale Camera zoom factor
Quality Resolution scaling of the scene
Use Dynamic Quality Use a different resolution scale when moving the camera. Suitable for heavy scenes.
Quality 2 Resolution scaling of the scene when the camera is moving
  • Clipping
../../_images/gclp.png
Option Details
None All atoms are shown
Slice Only atoms in the bounding plane + thickness is shown
Cube Only atoms in the bounding volume is shown
  • Effects

Additional effects to apply to the scene

../../_images/geff.png

List of effects available:

  • Glow
Option Details
Threshold Minimum brightness value
Radius Blur radius
Strength Additive strength
  • Ambient Occlusion
Option Details
Samples Number of samples to average
Radius Radius for sampling
Strength Darken intensity
Blur Blur radius before darkening
  • Depth of Field
Option Details
Distance Focal distance from camera
Aperture Blur amount
Iterations Number of blur operations. Larger number is slower but reduces artifacts

Render Tab

  • To Image (GLSL)

Produces a high resolution screenshot of the view.

../../_images/rimg.png
Option Details
Width Width of the image (maximum 16k)
Height Height of the image (maximum 16k)
Slices Render in parts, improves render speed when the image resolution is very large
MSAA Averages the final image over 4 samples. Slower but more beautiful.
  • To Video (GLSL)

Produces a high resolution screenshot video of the animation playback.

../../_images/rmov.png
Option Details
Format Video format (GIF / AVI / PNG sequence)
Width Width of the video (maximum 16k)
Height Height of the video (maximum 16k)
Slices Render in parts, improves render speed when the video resolution is very large
MSAA Averages the final image over 4 samples. Slower but more beautiful.
Max Frames Maximum frames to render. Snapshots will be skipped if there are too many frames.