[Chimera-users] map 3d pdf

Tom Goddard goddard at cgl.ucsf.edu
Fri May 23 16:26:13 PDT 2008

Richard Newman wrote:
> Hi Tom
> Does CHIMERA have the ability to export a map format which can be used 
> by 3D PDF?
> We would like to make the EMDB maps available in this format.
> All the best
> Richard

Hi Richard,

  Chimera can export map surfaces in several 3-D file formats Wavefront 
OBJ, POV-Ray, RenderMan, VRML, or X3D using menu entry File / Export 
Scene....  The format for objects embedded in 3D PDF is called U3D which 
Chimera does not export.  I used a program called MeshLab to read OBJ 
format produced by Chimera and write U3D format, then used another 
program to convert LaTeX to PDF (pdflatex).  Here's an example showing 
EMDB map 1356.  It requires Adobe Acrobat Reader 8.0.  It will not 
display on Mac OS 10.4 Preview.


Producing the file was painful and Chimera can't export the surface 
coloring in OBJ format.  I think it would be more interesting for the EM 
Databank to show 3D models in the web browser like JMol shows PDB 
models.  I don't know if a java applet has been written to do that.  
Perhaps JMol could do it.


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