pKa display defects for 3D molecules

User 25d107bd42

17-10-2010 09:13:16

Hi, MarvinSketch has a very helpful and valuable tool: Tools - Protonation - pKa, but using it for 3D molecules, the display of the results is nearly unreadable, see attached screenshot.

Opening a *.mol file for a molecule coming from another program, f.e. from a quantumchemical calculation, one gets the molecule in 3D. In the normal canvas of MarvinSketch you can handle it as usual. But now using "Tools - Protonation - pKa" you get the molecule in windows with black background, the blue pKa-values are nearly unreadbale.

And: The microspecies columns show molecules without hydrogens, and this in a display, where the hydrogens play the chemistry.

Obviously here is once more used the mini-version of MSpace. That's not really the problem. The problem are the default settings for this. One can change this display using the right mouse button and in the three steps you can change the display to an acceptable version, as shown in the attached image.

But for the microspecies one cannot change the display. For the microspecies no hydrogens are shown and the charges are so tiny, it is nearly impossible to analyse the structure of the microspecies. (BTW: The tiny charges are an old problem of MarvinSketch).

I think, it must be easy to change the defaults for the displays. The program obviously recognizes, there comes a 3D molecule and changes the display from 2D to 3D, but with wrong defaults.

Regards, Hans-Ulrich

ChemAxon e08c317633

19-10-2010 10:38:11

Thanks for the suggestion. We decided to display the pKa results in 2D, even if the structure in MarvinSketch is a 3D structure. It will be implemented in Marvin 5.4.x.


User 25d107bd42

26-10-2010 17:15:46

Hi Zsolt, to wait on 5.4.x with unknown variable x is to long.

As a Java programmer I think, it must be easy to change the display options. Obviously the pKa tool uses the "mini-version" of MarvinSpace. And calling it from the pKa-display class there must be an "init" method starting MSpace. And in this "init" method the default variables are initialized. Change these to the other better options mentioned above and all is OK.

Best regards, Hans-Ulrich

ChemAxon e08c317633

02-11-2010 21:04:14


Unfortunately, we cannot implement this in Marvin 5.4., sorry.


User 25d107bd42

03-11-2010 18:16:24

Hi Zsolt,

it is not a good plan to display the pKa results in 2D coming from 3D. For many molecules it would give ugly displays and often you would not recognize the original structure. And it's a waste of programming and computer time.

Using the naming tools on the same molecule the hydrogen atoms are displayed and there is a really good presentation, see attached screenshot.

Why is the pKa tool not using the same display procedure as the naming tool ?

It must be easy to implement this change.

Best regards, Hans-Ulrich

ChemAxon e08c317633

05-11-2010 20:24:50

Hi Hans-Ulrich,

Thanks for the suggestion, we will rethink our previous decision.