Hi James -
If I remember correctly, PyMOL's IDTF output currently only supports triangles
meshes (not cylinders or spheres, e.g.), so unfortunately you're basically
limited to surface representations for output directly into that format.
As a workaround, you could try saving your scene in COLLADA format (`save
myfile.dae`), and use an external program (e.g. Blender, Meshlab) to convert to
IDTF or U3D. When doing so, please note that you'll probably need to `set
collada_geometry_mode=1` to specifically use the subset of COLLADA elements
supported by those two programs (they only allow <polylist> elements to
describe the triangles, which are a more general, verbose description than the
more concise <triangles> and <tristrips> output generated with the default
setting).
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Columbia University
On Mar 12, 2016, at 11:24 PM, James Kress
<jimkress...@kressworks.org<mailto:jimkress...@kressworks.org>> wrote:
Among the export functions, a particular interest of mine is the as a
idtf file as "precursor" for a 3d pdf mentioned at
http://www.pymolwiki.org/index.php/3d_pdf
where I experience difficulties I want to address here.
While the export via the CLI works fine for creating a *.png picture
or a VRML *.wrl-geometry, the similar export as *.idtf creates only a
header to describe the scenery, but not the (expected) spheres and tubes
to represent atoms and molecular bonds. The file generated is the same,
regardless if I request the data export via
save /home/user directory/target directory/test.idtf
or the recommended
save /home/user directory/target directory/test.idtf,*
Marking/highlighting the molecule in question does not alter the situation.
The relative orientation of the model in regard to the observer is
provided, however, in the programs command line, like
3Daac=20.0, 3Droll=0, 3Dc2c=0 0 1, 3Droo=50.00, 3Dcoo=0 0 -50.00
In addition, there is no *.tex file written -- well in contrast to the
pymol-wiki page -- that I would expect to be created in the very same
directory, too. (This is contrast to jmol offering export as *.idtf
while simultaneously writing a *.tex file, too.) Should I look up in a
different directory instead? May be a mistake during the installation
be a reason why I do not obtain (yet) a functional *.idtf? Do I need to
load another / an additional plugin to enlarge the export functions?
Thanks.
Jim
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