Re: [PyMOL] Get surface coordinates

Hi Jared,

So COLLADA exports some kind of already rendered 3D image.

Took me some time to figure out if dump exports the map points or something
specific to the surface representation. In fact, it is yet to be figured
out.

Dump can export at least map and surface objects.

When I export two different overlapping surfaces of the same map there is
points of the outer surface that aren't in the inner. I expected all points
of the inner to be present in both dumps.

So I guess that when I dump surface objects it exports newly created points
of the enclosed volume of that surface. Is it correct?

To export the map directly would preserve the original points? (Which I
hope to be the original grid count of the server's method)

Is overlap is defined for map objects?


Sorry maybe I'm not saying very clear.

And about the get_volume_field(), if I remember correctly it returned on a
call an ndarray of shape (28, 26, 15) and on other call an ndarray of shape
(28, 28, 16). Something like that.


Cheers,


Em sex, 1 de nov de 2019 10:33, Jared Sampson <jar...@co...>
escreveu:

> 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
> <)." rel="nofollow">https://github.com/schrodinger/pymol-open-source/blob/master/layer1/COLLADA.cpp#L667>).
> 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
>