Hi Gary and Thomas -
As Thomas mentioned, the sphere/cylinder/etc. primitives described in the
COLLADA 1.5 spec as <brep> ("boundary representation") elements would be the
best option for spheres and basically all other PyMOL representations except
for molecular surfaces. Unfortunately COLLADA 1.5 is not well supported by
other graphics applications. However, there is still room to optimize the
storage within the constraints of COLLADA 1.4.After looking through a couple test .dae files to refresh my memory, I see that the output from PyMOL does use <instance_geometry> elements. However, as Gary has noticed, it defines a separate <geometry> element for each sphere in the scene. This adds up quickly for scenes with many atoms represented as spheres. FWIW, the reasoning behind this when I originally wrote the COLLADA exporter was that color information is included in the <geometry> definition, and it was easier to write a separate geometry for each sphere than to collect information about all the different colors of spheres. Of course, it is possible to do this more efficiently. Probably the simplest way to cut down the file size would be to write only a single sphere <geometry> element *per color* of sphere present in the scene, and then use instances of those to represent all spheres that share the same color. The attached files each have two geometries (output by PyMOL with pseudoatom spheres at position=[0, 0, 0] and [1, 0, 0], in grey90 and red, respectively). The first file, "test.dae", was output directly by PyMOL and has one instance of each sphere, for a total file size of 21545 bytes. Manually adding a second instance of each sphere (translated by +/- 4Å along the X axis) in "test-added.dae" adds only 1147 bytes to the file (look for <node id="node-geom0-added"> and <node id="node-geom1-added"> in your favorite text editor), compared to adding 18174 bytes if the two additional spheres are exported from PyMOL with their additional geometries by adding additional pseudoatoms (that file not attached). That's an almost 94% reduction per added sphere; for scenes with many spheres, the storage savings would be substantial. On the other hand, if there is a way for color to be specified separately from the <geometry> element (which I imagine must be possible, but I haven't found a clear example of how to do this), that would be the most preferred option, as it would allow us to use a single sphere <geometry> element per output file. Thanks to Gary for bringing this up. Thomas, perhaps we can talk offline about what might be the best way to implement this? Cheers, Jared On June 6, 2018 at 2:24:08 PM, Thomas Holder (thomas.hol...@schrodinger.com) wrote: Hi Gary, Do you know an application which can actually read COLLADA files with sphere primitives? We've faced the problem that most tools only handle COLLADA 1.4, so if PyMOL would use COLLADA 1.5 features, the programs we know wouldn't read the exported files. See https://pymolwiki.org/index.php/COLLADA#Limitations I fully agree that sphere primitives and other COLLADA 1.5 features would be better (smaller files, precise sphere representation, etc.). Thomas > On Jun 6, 2018, at 1:19 PM, Gary Oberbrunner <ga...@darkstarsystems.com> > wrote: > > The collada file exported by pymol would be smaller and export/import faster, > I think, if it used geometry_instance for spheres rather than giving each > sphere its own geometry/mesh/accessors/etc.. Has that been discussed before? > > -- > Gary Oberbrunner -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
test.dae
Description: Binary data
test-added.dae
Description: Binary data
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