Hi Pedro -
The COLLADA option exports unlabeled mesh objects so I couldn't figure out
which one is acceptor or donor.
Yes, you're correct about that. This is due to the fact that COLLADA export
uses geometry after it is prepared for ray tracing, which doesn't know about
object names (see the primary function call). It might be interesting/useful
to export things in a more granular way using pre-ray-tracing information as it
is stored in the PyMOL session, but that would involve substantial effort, and
wasn't included when we planned this export feature.
If you wanted to know which mesh is which, you could export objects
one-at-a-time by disabling all the others, although to me, the dump command
output looks more helpful as it can be more easily parsed.
Just one more question, what are these normal values?
The normal values Thomas refers to are the 3 components of the vector
indicating the direction toward the "outside" of the object, which is normal to
the surface the triangle mesh attempts to approximate. This is used in shading.
https://en.wikipedia.org/wiki/Vertex_normal
The cmd.get_volume_field() returns a sparse ndarray with unknow layout and all
dimensions variables depending of the object. How to interpret such array?
On PyMOL 1.x it returned -1 but in 2.x returned the array.
The dump command worked (almost) like a charm.
I expect to extract the "dump" array from get_volume_field() so don't need to
write the file just to be read and deleted afterwards. Is it possible?
I'm not familiar with `cmd.get_volume_field()`, so I'll defer to others on
those questions.
Hope that helps.
Cheers,
Jared
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