Hi again! Thank you for all the answers from last time. It was very helpful. I have another question. I was trying to save extra attributes on a marker model from a cmm file and ran into some issues. I made a function to test it out using: marker_set.save_marker_attribute_in_sessions('marker_extra_attributes', Dict[str, str]) and got an error: ValueError: error processing: 'attribute registration' -> : No bundle information for typing._GenericAlias File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\session.py", line 262, in discovery raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) Is it only possible to save more primitive types or can I fix this somehow? In my project the cmm files contain extra attributes that my plugin makes use of. These are the attributes that I would like to save in sessions. I would like this save enabling function to be called automatically when a cmm file is opened so that I can enable saving of these attributes on file open. Is there perhaps some onFileOpened that I could subscribe to, or is there another way that could allow me to achieve this? -William fre. 27. aug. 2021 kl. 22:15 skrev Tom Goddard <goddard@sonic.net>:
Hi William,
To add a marker to an open marker set:
from chimerax.markers import MarkerSet marker_sets = session.models.list(type = MarkerSet) m = marker_sets[0] xyz = (15.3, -34, 8.8) color = (255,0,0,255) # RGBA 0-255 range. radius = 2.5 m.create_marker(xyz, color, radius)
I see MarkerSet is not in our online programming documentation yet. The source code is in your ChimeraX distribution under
chimerax/lib/python3.9/site-packages/chimerax/markers/markers.py
or on GitHub
https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/markers/src/marker...
The marker_extra_attributes is saved and restored in cmm files. For ChimeraX session files you can get extra attributes to save by saying what attributes you want saved
marker_set.save_marker_attribute_in_sessions('myattribute', float)
For placing geometric surfaces in the scene look at the shape command
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/shape.html
Surprised there is no cube shape, but maybe rectangle with the slab option can make a cube. Python code is here
https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/shape/src/shape.py
for example
from chimerax.shape.shape import shape_rectangle model = shape_rectangle(session, width = 10, height = 10, slab = (-5,5), mesh = True)
Tom
On Aug 27, 2021, at 8:21 AM, William Hofsøy via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi, I'm currently working on a plugin that deals with a cmm-file model and have a few questions about how to do certain things. Mainly I would like to be able to modify the model by adding new markers and links to the model. I have managed to figure out how to make new markersets and add them to the session but not how to alter existing ones aka the model that I load from the cmm file. Additionally I am making use of the marker_extra_attributes info since the cmm file im reading has attributes there that I need, but as I read in the documentation these aren't saved in sessions and I wondered if there is a way to do just that. Lastly, I was wondering if it is possible to place any mesh in the scene, for instance a cube.
-William _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users