Hello, I want to do an occupancy analysis of a rigid ligand in a MD trajectory. I used the MD Movie > Analysis > Calculate occupancy tool, and obtained the volume maps of each heavy atom of the ligand. To check, I also used the gmx spatial tool from GROMACS and the VolMap from VMD, to obtain the grids for the whole ligand, which have basically the same shape. This grid has a characteristic shape showing that particular orientations are stable through the MD run. I want to extract representative structures of these orientations, something like an "occupancy clustering". Note that I say orientations and not conformations. Since the ligand is rigid, there is no point to calculate the RMSD. So, what I want is to calculate clusters of orientations of the ligand in the binding site. Is this possible with Chimera? Thanks in advance, -Yasser