electron-flow source and sink visualization

Hi,





One of our users has pointed out that, under certain circumstances, students can be misled about where their electron-flow arrows are originating and pointing. The attached document illustrates the problem. Specifically, compare Scheme 1 to Scheme 2 and Scheme 3 to Scheme 4. The differences are that in Scheme 1 and 4, the user has clicked on a bond, whereas in Schemes 2 and 3, the user has clicked on an atom. The only visual difference between the structures is the originating point of the arrow, and it is difficult to discern that difference.





A solution would be to highlight the source and sink of an electron-flow arrow in some way when a user mouses over that arrow. Bonds could be highlighted with blue parentheses and atoms with blue circles, or both could have their color changed to green. I leave it up to you to decide what is the best visual cue. But I think it is important to add one.





-- Bob

We will investigate it.

Arrows are highlighted since this feature exists in Marvin... I think the real problem is the nonzero value of the tailSkip attribute. Currently, the value of tailSkip and headSkip is 0.15 for bonds and 0.25 for atoms. Scheme 1 would look better is tailSkip = 0 would be used for bonds. What do you think?

Yes, arrows are highlighted, but not the sources and sinks of the arrows.





I'm not sure what you mean by tailSkip, but if you mean the gap between the bond and the arrow, that's not the problem. The problem is seeing where the tail of the arrow begins. See the image below. It's very difficult to see that the arrow begins at the bond, not at the atom. Sure, if you look closely, you can see it, but unless you know to look for it, it's unlikely you will notice it.





What I'm suggesting is that mousing over the electron flow arrow highlights not just the arrow, but also the source and sink associated with that arrow.





I'd also like to suggest that it be possible to delete MPolylines when just one end or just the midpoint is highlighted. It's sometimes exceedingly difficult to delete a graphical or electron-flow arrow because it's hard to place the mouse so that both endpoints and the midpoint are highlighted.

Increasing the number of different highlighted things increases the confusion, not the visibility. Moreover, it would only apply to sketcher and not the exported images like the one you attached here. So I think it would not solve anything.


Seeing that the arrow begins at the bond is possible if it begins at the center of the bond. So the problem seems to be the presence of that gap. On your attached image, the beginning of the arrow would be in the center if there was no gap.

cspeter wrote:

Increasing the number of different highlighted things increases the confusion, not the visibility. Moreover, it would only apply to sketcher and not the exported images like the one you attached here. So I think it would not solve anything.

For our purposes, it does not have to apply to exported images. It needs only to apply to the sketcher.





If you are worried about the possibility of confusion when multiple items are highlighted, how about creating an option, settable by the user or apple initialization parameters, that specifies whether sources and sinks should be highlighted when mousing over arrows?





Or, how about control-clicking on an electron-flow arrow causes the sinks and sources to be highlighted?

Quote:

Seeing that the arrow begins at the bond is possible if it begins at the center of the bond. So the problem seems to be the presence of that gap. On your attached image, the beginning of the arrow would be in the center if there was no gap.

Even in that case, the arc of the arrow would pass through the O atom, making it look like it originated at the O atom, not the C=O bond.





And yes, students can alter the arc of the arrow so that it no longer passes through the O atom. But that assumes that they notice the problem in the first place. I'm trying ot come up with an easy way for them to see where the electron-flow arrows originate.

Atom pair type line (and arrow) end points are highlighted differently, the circle in the center of bond is replaced by a rectangle, see the attached screenshot. It is only implemented in the Marvin 4.2 development branch. Is this solution suitable for you?

It seems to be acceptable, but I will know for sure only once I try it out. Let me know when you have created a build that contains this feature so that I can try it out.