ChimeraX Recipes

Mark Connected Pieces of a Surface

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 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/
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] =[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 =
    markers = [marker_set.create_marker(center, color, radius) for center in scene_centers]
    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)


Tom Goddard, October 8, 2020