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).

• write command
• Pop-up menu
• save isosurface command

MOL format

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:

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

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.).

Contributors

AngelHerraez