Please confirm these are the steps you follow:
1. sketch a molecule
2. select "Tools->Protonation->pKa" from the menu
3. press "OK" on the options panel
The calulation is run, and the calculation result is shown.
4. close the options panel (the result window is closed too)
5. modify the compound sketched
6. select "Tools->Protonation->pKa" from the menu
The options panel and the result of the first calculation appears (the result which appears is not the result of the second calculation, second calculation is not run yet).
To run the calculation on the second (modified) molecule press the "OK" button on the options panel. I hope this helps, and sorry for the inconvenience.
Anyway, the results of the previous calculations should not be shown when the options panel pops up. This is a bug, we will fix it. Thanks for the report.
Yes, this is the workaround, as I mentioned earlier in this post:
To run the calculation on the second (modified) molecule press the "OK" button on the options panel.
In fact, the problem is that the result windows are stored with he options panel. When the options panel is shown for the second time, then the previously calculated results are displayed also. We will fix it.
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