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