Hi Thomas,
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?
Hi Jared,
The COLLADA option exports unlabeled mesh objects so I couldn't figure out
which one is acceptor or donor.
Em qua, 30 de out de 2019 às 15:20, Thomas Holder <
thomas.hol...@schrodinger.com> escreveu:
> Hi Pedro,
>
> There is a "dump" command which exports all surface points and normals to
> a text file.
>
> dump /tmp/dump.txt, acceptor_17
>
> Each line will have 6 numbers, 3 for the position, and 3 for the normal.
>
> For cmd.get_volume_field you need the map name, not the surface name.
>
> data = cmd.get_volume_field('acceptor')
> print(data)
>
>
> Hope that helps.
>
> Cheers,
> Thomas
>
>
> > On Oct 30, 2019, at 6:42 AM, Pedro Lacerda <pslace...@gmail.com> wrote:
> >
> > And cmd.get_volume_field is returning -1.
> >
> > Em qua, 30 de out de 2019 às 02:00, Pedro Lacerda <pslace...@gmail.com>
> escreveu:
> > Hi,
> >
> > How can I access the underlying coordinates of acceptor, donor and
> apolar surface objects on the given session given by the following server?
> Coords akin to dot representation would suffice.
> >
> > http://fragment-hotspot-maps.ccdc.cam.ac.uk/results_table
> > http://fragment-hotspot-maps.ccdc.cam.ac.uk/result/1542
> >
> > An example of session is attached.
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> >
> > ARSB_hotspots.pse
> >
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > _______________________________________________
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
--
Pedro Sousa Lacerda
*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*
*@pslacerda*
*+55 71 9 9981-1856*
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