Backward compatibility

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Revision as of 17:32, 17 January 2009 by AngelHerraez (talk | contribs) (Hydrogen bonds: calculation and display)
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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.

Contributors

AngelHerraez