delete terminal bond without deleting terminal atom

As I'm writing mechanism-type questions for students, I often have to delete terminal bonds without deleting the terminal atom. For instance, in a Finkelstein reaction I have to create a C-I bond and break a (terminal) C-Br bond.

I can't figure out how to do that in MarvinSketch. The only way I can figure out how to get the image I need is by deleting both the terminal bond and atom, then replacing it with a new Br atom (Br ion, actually). The problem I have with that is that the atom numbering in the MRV/XML is affected by that so that I can't use an XML parser to check differences between my solution and a student's answer.

Is there any way to delete just a terminal bond, but leave the terminal atom in place?

 

MarvinSketch 5.2.4 on XP SP3

Hello,

Unfortunately, there is no way to delete a terminal bond without deleting the terminal atom. Copying the terminal atom before delete might help you to save the atomic attributes like charge, but not the indices. Molecule-editing steps, like deleting a bond, usually modify atomic indices.

Best regards
Erika.

Erika wrote:

Hello, Unfortunately, there is no way to delete a terminal bond without deleting the terminal atom. Copying the terminal atom before delete might help you to save the atomic attributes like charge, but not the indices. Molecule-editing steps, like deleting a bond, usually modify atomic indices. Best regards Erika.

Is there any way to include this as a "feature" at some point in the future?

When teaching reaction mechanisms, students learn to make and break bonds ("pushing electrons"), but they shouldn't have to redraw any atoms. In fact, it leads to a great deal of confusion since atoms are supposed to be stationary in reaction mechanism descriptions (only electrons move around).

Thanks.

We will consider your request and get back with an answer after the holidays.

Best regards,

Erika.

One idea for implementing this feature: if the user holds down the option or control key when deleting a bond, then terminal atoms are not deleted.  If the user does not, then they are.  This implementation would preserve the current behavior while making available the requested behavior.  Even better, you could provide an option in the Preferences dialog and via MarvinSketch parameters to switch the meanings of the two keystrokes.  

Hi,

Thanks for your suggestion, we registered this feature request in our system.
We will notify you as soon as the feature is implemented.

Regards,
Erika

Hi Bob,

This feature has already been implemented, and available in 5.4: If you hold down the Alt key when clicking on a terminal bond with the Delete tool, the terminal atom is not deleted. The default can also be changed, at Edit > Preferences --> Bonds tab.

Best regards,

Akos

There is no Alt key on a Mac.  Is there an equivalent keystroke?

Hm, are you absolutely sure, Bob? There's an alt key on my MacBook just next to  ctrl, left to the command (apple) key. And the bond deletion worked as Akos described.

 

BR

Miklos

There is an alternative way to delete bonds without deleting the terminal atoms, already implemented in 5.3.* versions: right button click over the bond and select delete in the popup menu.

Zsuzsa

mvargyas wrote:

Hm, are you absolutely sure, Bob? There's an alt key on my MacBook just next to  ctrl, left to the command (apple) key. And the bond deletion worked as Akos described.   BR Miklos

Oh, got it.  I see that Apple now uses the option key as the PC alt key for Windows emulation.