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).
- Pop-up menu
write command: MDL formats
Jmol can export the currently selected set of atoms to a file in
- MOL v2000 format (single model)
- MOL v3000 format (single model)
- SDF v2000 format (single or multiple models)
according to the official format specification from MDL-Symyx-Accelrys.
(Jmol version 12.1.26 has this full set of options; former versions export only MOL v2000 and match the specification only partially.)
The syntax (see reference documentation) is
write myFile.mol #exports to MOL v2000 write v3000 myFile.mol #exports to MOL v3000 write myFile.sdf #exports to SDF v2000
write mol myFile.myExt #exports to MOL v2000 write v2000 myFile.myExt #exports to MOL v2000 write v3000 myFile.myExt #exports to MOL v3000 write sdf myFile.myExt #exports to SDF v2000