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... <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 <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