No hydrogens in tools-pKa-display coming from 3D

Hi, yesterday in a student course we built R-lactic-acid, analysed the stereochemistry and then we used the tool pKa. The result can be seen in the attached image. It was disappointing, all hydrogens have gone and only tiny minus sign designate the anions.

I know, this is a problem of the 3D display (MSpace ?), but both MarvinSketch options View - Open-MarvinView2D and MarvinView3D show all hydrogens. Why does the pKa tool use this bad display ?

I know, 2D-structures are displayed with all hydrogens in the pKa-tool with correct hydrogens for the acid and the anions. But it is counterproductive when you must "downgrade" the 3D structure to 2D before doing pKa.

Regards, Hans-Ulrich

Dear Hans-Ulrich,

Before pKa calculation is started all explicit hydrogens are implicitized, because our pKa calculation algorithm requires molecules in such form. Taking care of correct visualization of hydrogens in 3D is not supposed to be the task of the pKa calculator plugin. Please accept this as a reasonable limitation of the plugin.

Regards,
Zsolt

Dear Zsolt, OK. I will explain it in this way to the students.

Thank you and regards, Hans-Ulrich