drawing electron-flow arrows

In most respects, MarvinSketch is superior to Marvin JS. However, I must admit that the way Marvin JS implements drawing electron-flow arrows is far superior to MarvinSketch, for several reasons.

1. In Marvin JS, if you want to draw an arrow from atom A to an incipient bond between A and atom B, you click-hold on A, then drag to B, then release, and the arrow snaps back to the incipient bond. By contrast, in MarvinSketch, you click or click-hold on A, then drag the cursor to between A and B until Marvin identifies which atom you want to be atom B. The problem is, in an even moderately uncrowded drawing, Marvin can identify any number of atoms as atom B. (For example, in the drawing whose MRV is reproduced below, try drawing a one-electron arrow from the lefthand O· to between that O and the H atom below it.) The Marvin JS method is unambiguous. 


2. In Marvin JS, you can toggle the arrow from pointing to between A and B to pointing directly to B, simply by clicking on the arrow with the arrow-drawing tool. There is no such capability in MarvinSketch.


3. If you draw an electron-flow arrow from an A–B bond to an incipient bond between A and C, it is easy to mistakenly place the bond between B and C. In MarvinSketch, you have to erase the arrow and try again. In Marvin JS, you merely click on the arrow, and it changes from pointing between B and C to pointing between A and C. 

It would be great if you could change MarvinSketch so that it had these Marvin JS features as well.

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Dear Bob,

Thank you for the feedback! We do appreciate and will think about how to unify, in terms of functionalities, the sketchers. 

Best regards,

K

I'm sorry, but I must complain about how recent versions of MarvinSketch handle the drawing of electron-flow arrows to incipient bonds. If I have a crowded drawing, it is nearly impossible to draw an electron-flow arrow to point to a desired incipient bond; it seems that MarvinSketch wants to make the furthest possible atom the second atom of the incipient bond. For example, in the attached drawing, try erasing the one-electron arrows and then redrawing them to point to the same places. You'll see it's impossible. (It doesn't matter whether you draw them as one-electron or two-electron arrows.) To draw the arrows in this figure, I had to point the arrows to the desired atoms, then edit the MRV directly to get them to point to the incipient bonds! That should not be necessary! Nor should it be necessary to have to draw each step individually in one window, then copy it and paste it into another window with all the other steps.

Marvin 15.4.27 does not have this problem. You must have changed the algorithm for finding the other atom of the incipient bond sometime after April last year. Please change it back!

No comments?

bobgr wrote:

No comments?

Hello,

An internal ticket has been created and waiting for schedule.

Sorry for not communicating it back then.

 

Kind regards

Zsolt

Any progress on fixing this inefficiency? I know that you're not developing the Marvin applet anymore, but you said you're continuing to develop the desktop version, and this problem makes the desktop version nearly impossible to use when drawing multistep mechanisms (as opposed to a short, one-step mechanism). I need to use an older version of Marvin (15.4.27) if I want to draw a multistep mechanism with many structures and electron-flow arrows. I know that it should not be too hard to fix this problem, because it was introduced only fairly recently, so you should be able to revert to an older algorithm for finding a potential incipient bond.

Unfortunately we were not able to fix this yet. However, if you zoom to level 200% it is solves the problem.

Best regards,

Efi