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

Atom line

The top line is an example of Jmol 12.1.26 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

d = mass difference (isotopes)

c = formal charge code

Some software pieces are more forgiving than others in reading MOLfiles. For example, PowerMV (a freeware viewer for SDF files; DOI:10.1021/ci049847v) fails to open files exported by Jmol. (SDF format is identical to MOL format, except that it supports more than one model, so one just needs to rename the file to have PowerMV try and open it.)

Jmol export can hence be improved in producing this format:

• For atoms, shift the position of the coordinates so that the decimal point is at the right place. Reduce the number of decimals accordingly.
• For atoms, add the trailing zeros that represent extra, optional, data.

Proposed output (satisfies PowerMV input):

 3.6133866 2.2537918 -2.035789 C   0  0
xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee

All the extra zeros could be added for a better compliance, but that would increase the file size.

Bond line

The top line is an example of Jmol 12.1.26 output in each bond's line of a MOL file, while the bottom line is the specification by MDL/Symyx:

  1  2  1
111222tttsssxxxrrrccc

1,2 = atoms bonded (atom numbers)

t = bond type

s = stereo type

x = not used; r,c = specific to MDL database query

Jmol export can also be improved in producing this format:

• For bonds, add the trailing zeros that represent extra, optional, data.

Proposed output (satisfies PowerMV input):

111222tttsssxxxrrrccc
  1  2  1  0

End records

Jmol export can also be improved:

• Add the end record "M END".
• Add the end record "$$$$" needed for SDF-format compliance.

Contributors

AngelHerraez