Re: [PyMOL] The Wiki appears outdated or in error

[James K. <jim...@kr...>]

Bob,

 

Thanks for the note.  The pdf files you generated were quite nice.  I just cannot get the quality of output you got using the PyMOL to dae to u3d to pdf path.  All I get are washed out colors.  No surface properties (shine, specular, etc.) at all.

 

PDF3DReportGen is the only software I have found that can give me close to the representation I need.  Even then, I have to use VMD, export to obj and then import to PDF3DReportGen to get good quality graphics.

 

Very discouraging.

 

Jim

 

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From: Robert Hanson [mailto:ha...@st...] 
Sent: Saturday, April 02, 2016 1:14 AM
To: jim...@kr...
Cc: Thomas Holder <tho...@sc...>; pymol-users <pym...@li...>
Subject: Re: [PyMOL] The Wiki appears outdated or in error

 

In case you are interested, Jim, Jmol will read (most/some) PyMOL session files, and Jmol can then create both an idtf for generating a u3d file, and a small sample TeX file also that can be used to create a PDF containing it. 

I had some interest in u3d back in 2009, when I wrote this exporter. You might be interested in my notes at the top of https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/export/_IdtfExporter.java 

Here are a few examples created using Jmol: http://chemapps.stolaf.edu/jmol/u3d/

As I recall, the TeX file is necessary in order to properly reproduce the viewport state.


My conclusion was that u3d is an absolutely unmanageable file format. Its construction is totally obtuse, and the idtf->u3d converter has bugs that will probably never be fixed. I could be wrong, and in the intervening years it has improved, but my impression at the time was that it was an experimental format out of Adobe's research labs that never really made it and hasn't been developed much since then. 

Its inclusion in PDF file quite frankly takes the "P" out of "PDF."

Bob Hanson

​