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pKa plugin in Marvinsketch 5.0.2.1
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David

Joined: 25 Jun 2007
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Link to postPosted: Fri Jun 20, 2008 2:00 pmPost subject: pKa plugin in Marvinsketch 5.0.2.1 Reply with quote

On windows XP, after running the pKa calculation, modify the compound sketched. Re-running the calculation just repeats the one done for the previous molecule, not for the modified one.
Zsolt
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Joined: 11 Jan 2006
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Link to postPosted: Fri Jun 20, 2008 3:24 pmPost subject: Reply with quote

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.

Zsolt
David

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Link to postPosted: Fri Jun 20, 2008 4:06 pmPost subject: Reply with quote

Yes, that's right, you do get the new calculation when you hit OK.
David

Joined: 25 Jun 2007
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Link to postPosted: Wed Oct 08, 2008 9:07 amPost subject: pKa plugin in Marvinsketch 5.1 Reply with quote

This bug is not fixed in 5.1 - is there a workround in 5.1?
David

Joined: 25 Jun 2007
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Link to postPosted: Wed Oct 08, 2008 9:15 amPost subject: Reply with quote

There is a workround, leave the pKa Options window open and hit OK on that window after modifying the structure, the pKa window comes up with the new structure.

If the pKa window option is closed before modifying the structure, you get back the original pKa window again, and have to hit on OK on the pKa Options window to get the modified structure pKa window.
Zsolt
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Link to postPosted: Wed Oct 08, 2008 10:52 amPost subject: Reply with quote

Yes, this is the workaround, as I mentioned earlier in this post:
Quote:
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.

Zsolt
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