Here is some ChimeraX Python code that puts a spherical marker at the center of each connected piece of a surface. Brandon Scott asked about this for tracking blobs in 3D light microscopy. I pieced to together this code by looking at two existing ChimeraX features: the mouse mode for placing a marker at the center of a connected surface piece, and the surface dust command that hides all small connected surface pieces.
This capability has been added to the ChimeraX distribution as the mark connected command.
The Python code mark_blobs.py when opened in ChimeraX defines the markblobs command. Here is an example use marking each blob of the X-ray density for PDB crystal structure 1a0m
open ~/Downloads/mark_blobs.py open 1a0m from eds markblobs #1 radius 0.2 color gold
Here is the bit that computes the centers
def surface_blob_centers(surface): ''' Return an array of center positions for each connected set of displayed triangles in the surface. Centers are in surface coordinates. A center is computed as average vertex position weighted by vertex area where vertex area is 1/3 the area of the adjoining displayed triangles. ''' # Get list of (vertex indices, triangle indices) for each connected piece triangles = surface.masked_triangles from chimerax.surface import connected_pieces, vertex_areas blob_list = connected_pieces(triangles) # Compute area-weighted center for each blob vertices = surface.vertices varea = vertex_areas(vertices, triangles) from numpy import empty, float32 centers = empty((len(blob_list), 3), float32) for i, (vi,ti) in enumerate(blob_list): blob_varea = varea[vi] blob_area = blob_varea.sum() centers[i] = blob_varea.dot(vertices[vi])/blob_area return centers
And here is some Python to define a command “markblobs” that runs this.
def markblobs(session, surface, radius = 0.5, color = (255,255,0,255)): centers = surface_blob_centers(surface) scene_centers = surface.scene_position * centers from chimerax.markers import MarkerSet marker_set = MarkerSet(session, name = surface.name) markers = [marker_set.create_marker(center, color, radius) for center in scene_centers] session.models.add([marker_set]) session.logger.status('Found %d connected surface pieces' % len(markers), log = True) return markers def register_command(logger): from chimerax.core.commands import CmdDesc, register, SurfaceArg, FloatArg, Color8Arg desc = CmdDesc( required = [('surface', SurfaceArg)], keyword = [('radius', FloatArg), ('color', Color8Arg)], synopsis = 'Place markers at center of each connected surface blob' ) register('markblobs', desc, markblobs, logger=logger) register_command(session.logger)
Tom Goddard, October 8, 2020