Hi Jared,
Only writing one sphere geometry per color makes a lot of sense, yes let's talk
about that offline! I also see some dispensable elements like <rotate> with
identity matrix, which we could safely remove to reduce file size further.
Cheers,
Thomas
> On Jun 6, 2018, at 10:49 PM, Jared Sampson <jared.samp...@columbia.edu> wrote:
>
> 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
>
> <test.dae><test-added.dae>
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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