Backward compatibility
Jmol intentionally keeps a strong backward-compatibility, that is, new versions try to maintain operative all things that could be done in older versions, with the same command syntax, and to also keep defaults.
However, on a few occasions there are stronger reasons to decide upon a change in the default behaviour; this can break existing scripts if you update the Jmol version.
This is a place to try and collect such discrepancies, for the benefit of the community of users and webpage/script programmers.
Please, add here any issues you have found when updating Jmol versions:
- Script commands that get broken when moved to a new version of Jmol.
- Changes in default behavior.
Make sure to specify the old and new version numbers across which the behaviour was changed.
Hydrogen bonds: calculation and display
Changed between: v. 10.0 and 10.2.
Description:
hBonds on does not calculate hydrogen bonds anymore. Instead, the first time you want hydrogen bonds displayed you must use hBonds calculate. This enables the separation of H-bond data present in the pdb file (e.g. specified by the authors as calculated by a separate algorithm) and H-bond information as calculated by the Jmol algorithm.
Effects:
Old scripts using hBonds on will no longer display any hydrogen bonds in most cases, or will display just a few of them (few pdb files include H-bonds specification).
Advice:
Where you had the first hBonds on command for a molecule, replace it with hBonds calculate. Where hBonds on was only to restore display (e.g. after a hBonds off), you can leave it as it was.
