Re: [Jmol-users] Wavefront OBJ Exporter for Jmol

[Robert H. <ha...@st...>]

On Fri, Jan 14, 2011 at 3:12 PM, Kenneth Evans <ke...@ke...> wrote:

>  Hi,
>
> I have written a Wavefront OBJ exporter for Jmol.  If you are interested, I
> would be happy to send the files.
>
> Some background:
>
> I have found the OBJ format to be the mostly likely format to be supported
> by 3D modeling software.  There is a list in the following reference:
>
> http://en.wikipedia.org/wiki/Wavefront_.obj_file
>
> and it includes most of the popular programs from Blender to Photoshop.
> This includes Maya, and the Wavefront OBJ exporter would likely be a better
> choice for Maya than the Jmol Maya exporter, I think.  I would also note
> that Pymol exports OBJ.
>
> The format is relatively simple, and the above link includes a good
> specification of the format.
>
> My reason for doing this was to get molecular models into 3D modeling
> programs.  The only Jmol format that is a viable candidate is U3D, obtained
> through the rather involved procedure described in your pages.  U3D is not a
> particularly popular format, and is supported mostly by Adobe.  This
> procedure clearly makes good PDFs, but I found the U3D files created are not
> very usable.  Photoshop (by Adobe ;-) does read U3D, but gets errors with
> all the U3D files I have tried from Jmol and fails to even read some of
> them.  This is probably not a bug in Photoshop, as I have found it to read
> very complicated U3D files from other sources than Jmol -> IDTF ->
> IDTFConverter -> U3D.  Whether this is a problem with the JMol IDTF exporter
> or the IDTFConverter, I cannot say.  IDTF is certainly not a popular format
> in any event.
>
>
IDTF is just a format they threw together because it was impossible for
anyone outside of Adobe to figure out how to construct U3D files, I think.
That format is incredibly tricky and not well described (in my opinion). So
they created IDTF as a way to U3D. It serves no other purpose.

I suspect it is a bug in their reader, actually. Or possibly IDTFConverter.
Hard to believe it's a Jmol bug -- since the IDTF is being converted to U3D
successfully (or so it would appear -- we could check that). Jmol does quite
a bit of cataloging of objects, and one could imagine a reader that is not
set up for that. But, yes, does seem odd that Photoshop does not like U3D
files created by Adobe's own converter.... It would be instructive to start
very simple (atoms only, no bonds, for example) and see if it still has a
problem.

Jmol reads Wavefront OBJ files, so it would be reasonable for it to write
them as well. I can't remember how the cataloging goes for those. It that is
not possible, we really shouldn't do much with it. Writing 10,000 individual
balls and sticks is not particularly practical.


> So I did the OBJ exporter.  It appears to work for ball-and-stick models,
> and works in all the 3D programs I have access to.  It implements all the
> outputXxx() routines necessary to do ball-and-stick.  I also implemented:
>
> outputCone
> outputTextPixel
> outputTriangle
>
> but I did not test them.  I am only a causal user of Jmol, and don't know
> what to use for test cases for these.
>
> I did not implement:
>
> outputFace
> outputSurface
>
> It would take too much time to figure out what these (surfaces at least)
> are supposed to do, and again, I don't have test cases.  It would probably
> be easier for a Jmol person, to look at what I did and fix it for surfaces
> or work with me a bit.  (This is, of course, assuming you are even
> interested ;-)
>
> As far as testing what I did, most of the 3D modeling programs are pricey
> and all have a steep and long learning curve.  Unless you already have one
> of these, MeshLab would be the best bet.
>
> My background is that, as mentioned, I am a casual Jmol user and not a
> Chemist nor Biologist.  I have an intermediate, not advanced, knowledge of
> 3D modeling programs.  It took less time to write the exporter than I spent
> messing around trying to make things work with the existing situation.
>
>     -Ken
>
>
I'd sort of like to only implement a full exporter, not one that is so
selective, but the Maya exporter is like that, too. Definitely interested. I
think the face/surface business would be relatively easy to implement.

Bob


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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900