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:
- On the Conversion tab, Enable Pentakis Sphere Options, set min=max=6
- On Advanced tab, adjust “General Font Size Scale” from 1.0 to a higher or lower value to get best label sizes.
- On Visual Effects tab, enable Specular Color, use color selector to set mid-gray (RGB 101,101,101)
- Also on Visual Effects tab, enable Shininess, set value to 5.0
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.