Converting Chimera X3D with Labels to 3DPDF

Molecular models from UCSF Chimera (UCSF Chimera Home Page) are best converted using the X3D format. PDF3D ReportGen and PDF3D.IO development SDK can be used to convert X3D format to 3D PDF. Labels may also be preserved.

Load the X3D file and then make some setting adjustments:

  1. On the Conversion tab, Enable Pentakis Sphere Options, set min=max=6


  1. On Advanced tab, adjust “General Font Size Scale” from 1.0 to a higher or lower value to get best label sizes.


  1. On Visual Effects tab, enable Specular Color, use color selector to set mid-gray (RGB 101,101,101)


  1. Also on Visual Effects tab, enable Shininess, set value to 5.0


Converting directly to 3D PDF is best, because information is placed in the PDF layer, the 3D layer, and also embedded JavaScripts are added to the document that control how interaction and labels are dynamically placed, sized and oriented in the scene. The default PRC-HCT creates the smallest and most efficient internal encoding for the PDF 3D scene.

If exporting a U3D file only, then the raw 3D geometry is exported without the JavaScripts or additional information needed in the PDF layer.

If using an external publishing system such as LaTeX, it is common practice to embed a U3D within the .tex document specification. However, to avoid loss of information during conversion we recommend an alternative approach, see the blog article:

If using an MS-Word (Office 2013 or later) document source, then the conversion can be assisted using a template placeholder method.