MarvinView and Implicit Hydrogens - Problem ?

Hi,

displaying C2H3N-isomers in MarvinSketch using "View - Open MarvinView 3D" I got the attached image.

MarvinView is able to show the triple bonds and it shows also lone pairs as double-dots. Both features are very good.

But using in this MarvinView version "View - Implicit Hydogens" is not possible. What am I doing wrong ?

Regards, Hans-Ulrich

In Marvin, the Ball & Stick visualization mode does not support displaying of implicit hydrogens. I recommend to select Wireframe, Wireframe with Knobs or Sticks mode if you like see the implicit hydrogens.

Hi,

trying these options, I found more inconsistencies, see attached screenshots.

1) The implicit hydrogens are shown for the options "Wireframe - WireFrame with Knobs - Sticks" and interestingly also for the option "Spacefill".

2) In all these displays the planar structure for the ketenimine is now wrong, NH must be orthogonal. As shown in my other actual topic https://www.chemaxon.com/forum/ftopic6633.html  the MarvinSketch - MarvinSpace 3D is able to show the NH=C=CH2 structure correctly orthogonal.

3) There is no difference between "Wireframe" and "Wireframe with knobs" and for "Sticks" the bonds are only a little bit thicker. The C in the middle of the ketenimine cannot be seen.

Regards, Hans-Ulrich

Hi Hans-Ulrich,

Thank you for sharing your experiences with us.

Regarding point 2, if you add the explicit Hs first, and then optimize it, it is wrong, but - interestingly - if you optimize with implicit Hs and then add the explicit Hs, it is correct. We will fix the 3D cleaning algorithm to properly calculate the location of the explicit Hs.

Regarding point 3: it is actually a bug in 2D: the knobs are missing from the view; we will fix it soon. (In 3D the knobs are there).

 

Best regards,

Akos