Hi Jared,
May I reopen the ticket?
I got the `get_volume_field` idea. It returns the grid. My grid was trimmed
or was justified to have only the observations and because of this my
shapes seemed incoherent.
I jumped in the code yesterday to add the `quiet` flag on `dump`. This is
code is like
Update:
worked the same for me, but may have impact in other cases:
MIN_LEVEL = 0
MAX_LEVEL = 20
LEVEL_RANGE = np.arange(MIN_LEVEL, MAX_LEVEL+0.5, 0.5)
def _get_map(map_name):
dump_fhandle, dump_fname = tempfile.mkstemp()
open(dump_fhandle).close()
try:
levels = {}
For the sake of completeness here is some working code.
`dump` exports the surface of map representations. They are all surfaces.
So I had to dump the map at each level (0.5 by 0.5 increment) in order to
get a filled volume. If you concatenate all xyz arrays you get the filled
volume of the
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
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
Just one more question, what are these normal values?
Em sex, 1 de nov de 2019 às 02:43, Pedro Lacerda
escreveu:
> 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
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
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 =
And cmd.get_volume_field is returning -1.
Em qua, 30 de out de 2019 às 02:00, Pedro Lacerda
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
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
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