I think as Elaine suggests just placing markers on the density map might get you started. I tried it using the ChimeraX Markers toolbar using place markers on Center mouse mode. Then just right-clicked 50 blobs to place markers, then used the Link markers mouse mode to connect a few, then wrote out an mmCIF file. All seemed doable. Of course the atom types, silicon vs oxygen are not distinguished but you could perhaps hand edit the mmCIF file to fix that.