Dear Chinh, I am not sure if you can do multiple (batch) conversions in chimera, but the tool you seek could be openbabel, using command line or openbabel gui. On the command line you can issue, for one molecule (it's for Linux): babel my.mol my.gzmat This creates Gaussian style Bond-Angle-Torsion a.k.a. Z-matrix coordinates. For batch processing, you can use: babel *.mol -ozmat -m Best regards, Vis