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delete terminal bond without deleting terminal atom
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Michiel

Joined: 23 Jan 2004
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Link to postPosted: Thu Dec 17, 2009 7:24 pmPost subject: delete terminal bond without deleting terminal atom Reply with quote

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




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Erika
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Joined: 12 Oct 2005
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Link to postPosted: Fri Dec 18, 2009 4:18 pmPost subject: Reply with quote

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.

Michiel

Joined: 23 Jan 2004
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Link to postPosted: Mon Dec 21, 2009 9:45 pmPost subject: Reply with quote

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.

Erika
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Link to postPosted: Wed Dec 23, 2009 10:28 pmPost subject: Reply with quote

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

Best regards,

Erika.

Bob

Joined: 15 Jun 2004
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Link to postPosted: Thu Dec 31, 2009 3:24 amPost subject: Reply with quote

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.  

Erika
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Link to postPosted: Tue Jan 05, 2010 12:42 pmPost subject: Reply with quote

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

Akos
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Link to postPosted: Thu Jan 06, 2011 5:00 pmPost subject: Reply with quote

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

Bob

Joined: 15 Jun 2004
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Link to postPosted: Thu Jan 06, 2011 5:11 pmPost subject: Reply with quote

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

Miklos
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Link to postPosted: Thu Jan 06, 2011 11:06 pmPost subject: Reply with quote

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

Zsuzsanna
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Joined: 12 Nov 2009
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Link to postPosted: Thu Jan 06, 2011 11:10 pmPost subject: Reply with quote

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

Bob

Joined: 15 Jun 2004
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Link to postPosted: Mon Jan 10, 2011 5:51 pmPost subject: Reply with quote

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.

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