Support for stereochemistry

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Jmol supports stereochemistry in some 2D file formats.

MOL formats

This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like mol, sdf, etc.

In the CTfile specification, stereochemistry is specified in the bond line, columns 10-12 (the 4th number in the row), with a numeric code (see the table). If the model is flat (2D, all atoms have Z=0) and the filter "2D" switch is used in the load command, Jmol v.12 will use the stereo information to build a 3D model. After that, the bonds will be assigned as single.

JME format

This (Peter Ertl's JME Molecular Editor) is only a 2D format, but allows specification of "up" and "down" wedge bonds (see the table). Jmol v.12 reads these and uses them when converting the model to 3D, which is done automatically upon load. After that, the bonds will be assigned as single.

Bond codes

stereo bond bond code in MOL file bond code in JME file
up 1 -1
down 6 -2