crossing bonds

Now that Marvin is more versatile with 3D structures, it would be nice if there were a small gap in bonds that crossed behind other bonds. See the figure, in which C-H bonds cross C-C bonds.

This feature is 2D only. Because 2D molecules are generally small. 3D molecules can be very large and gap calculation would slow down painting (~ N^2).


In 3D, I suggest to use sticks or ball & stick mode rather than wireframe.

cspeter wrote:

This feature is 2D only. Because 2D molecules are generally small. 3D molecules can be very large and gap calculation would slow down painting (~ N^2). In 3D, I suggest to use sticks or ball & stick mode rather than wireframe.

Maybe 3D molecules can be very large, but one that is being made into a 2D picture probably wouldn't be all that large. Anyway, the bond-crossing gaps are needed more in 2D projections of 3D molecules than they are in 2D molecules.





Perhaps you could check the size of the molecule before deciding whether to include the gaps. Make the size of the moelcule an option for the user to change.

It might be a good idea but I am not sure. The size of the applet's jar file should only be increased with a new feature (or new option) if it is really useful.


Why do you need wireframe at all? In the viewer, ball & sticks is the default for 3D. In the sketcher, only 2D editing is possible currently, so there is no point in sketching 3D structures. You are right, wireframe mode should be improved in the sketcher, as soon as 3D sketching will be possible. But at the moment, it is not the case...

cspeter wrote:

Why do you need wireframe at all? In the viewer, ball & sticks is the default for 3D. In the sketcher, only 2D editing is possible currently, so there is no point in sketching 3D structures.

I need 2D projections of 3D structures so that my students can learn to interpret 2D drawings in a 3D way.

Bob,


We will solve this somehow, but probably not in Marvin 3.5, because the release es very near and we are only fixing bugs now.

3D editing is under development. We will return to this problem before the next major release (Marvin 4.0).