My task is to identify ligand interactions with protein residues throughout an MD trajectory. I thought of something along the lines sel ligand z<3.5 #for vdW interactions, etc. I don’t think this can be done using the MD movie interface but I may be wrong. I then tried the following: 1. sel protein/hold selection steady 2. sel ligand 3. calculate occupancy (MD Movie/Analysis) 4. Chimera/select/clear selection 5. turned the Volume Viewer to mesh/level2. What I obtained is a mesh grid enclosing solid surfaces (see attached snapshot). I’m not able to get rid of these surfaces? I think that the problem ma be in step 2 above (sel :ligand). My ligand is N,N-Diethyl-meta-toluamide. Should I select the aromatic ring part separately of the amide part, run the above process and then repeat selecting the amide part? I also tried MD movie/Analysis/Residue interaction network, first selecting the ligand. The results I obtained are not satisfactory. Is there a better way of dealing with my problem? Thanks in advance for your kind help George