Chimera Tutorial:
How to Make High Quality Images

Tom Goddard
July 12, 2012

This tutorial shows settings for producing the best looking images in Chimera 1.6.

White Background Color Background Color Gradient
  1. Actions / Color / All Options...
  2. Click coloring applies to "background".
  3. Click color white.
  4. Alternatively use Favorites / Command Line, command "set bg_color white".
  1. Actions / Color / All Options...
  2. Click background "More..." button.
  3. Change Background Method from "solid" to "gradient".
  4. Click blue gradient button to change color scheme.
Volume Step Size 1 Adjust Transparency
  1. Show full-resolution volume data.
  2. Change volume dialog "step" to 1 (above histogram).
  3. Equivalent command "volume all step 1"
  1. Adjust surface transparency
  2. Click top histogram in volume dialog to choose
  3. Click volume dialog color button (square to right of "Color").
  4. Slide "A" slider to control opacity, 0.5 good.
Glossy Lighting Silhouette Edges
  1. Enable better quality "glossy" lighting.
  2. Tools / Viewing Controls / Lighting, Quality "glossy".
  1. Add black edges to surfaces.
  2. Tools / Viewing Controls / Effects, turn on "Silhouettes"
  3. Try silhouette width 3, press enter. Width is in pixels.
Save Large Image Shadows and Raytracing
  1. Resize window to desired aspect ratio and border width.
  2. File / Save Image...
  3. Change width or height to larger size, 2000 pixels high, press Enter.
  4. Press Save As.
  1. File / Save Image... has "Raytracing" option which produces shadows.
  2. Raytracing disadvantages:
    • Darkness and transparency will look different.
    • Trial and error required.
    • Slow to save image.
    • Multiple transparent surface layers always shown.
    • No silhouette edges.
  3. Interactive shadows. Tools / Viewing Controls / Effects.
    • Not available with some graphics card. Not on Mac.
    • Shadows may have rough edges.
    • May not work with glossy lighting.