OK, I've got it Jmol is not using the atom name for element identification; mol2 has an "atom type" field which seems to be both the cause and the cure. http://www.tripos.com/data/support/mol2.pdf
In your DMSO file, the atom type for the offending atoms is CT and H1. This is not supported by mol2 spec. See http://www.tripos.com/mol2/atom_types.html http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom_types.html If you cahnge that to just C and H, Jmol behaves. You should maybe use the proper types, which seem to be C.3, H, S.o, O.2 They also work in Jmol. > > I guess it is because the name of > > the atoms are the following: C1 H11 H12 H13 S O C2 H21 H22 H23 As I said, not that name, but the type at column 50. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
