File formats/Export

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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

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
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