File formats/Export

Exporting or saving molecular model files from Jmol

Although Jmol is basically a viewer, it has some limited capabilities to save files for the displayed molecular model (or a subset of it).

The top line is an example of Jmol output in each atom's line of a MOL file, while the bottom line is the specification by MDL/Symyx:

 3.6133866 2.2537918 -2.035789 C
xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee

Some software pieces are more forgiving than others in reading MOLfiles.

Jmol export can hence be improved in producing this format:

Shift the position of the coordinates so that the decimal point is at the right place. Reduce the numebr of decimals accordingly.
Add the trailing zeros that represent extra, optional, data (mass difference, formal charge, etc.).