Hello, I'm trying to use the clashes/contacts tool to explore valid phi/psi angles for L- and D-Ala (as part of a homework assignment; developing a Ramachandran plot for each). The tool worked great for L-Ala but does not report any contacts for D-Ala. (For each, I've snipped just the relevant sections out of a larger PDB. I'm using default params for collision detection, with detection calculated for any movement.) The difference in the PDB's for L-Ala and D-Ala is that the latter are in HETATM records. I did include the CONNECT info (to explicitly tell Chimera how HETATMs bond) but that did not help. Perhaps there's something else I must include, or some modification I can make to the HETATMS (element labeling?) so that collision detection will work as with peptides? Or is this a known limitation? (Is there a list of known limitations? I'm a new user.) I'm not Note that the distance tool works for D-Ala. If I can get collision detection to work, it take much less time. Thanks in advance. -Jonathan