Equilibrium Arrow Problems

I'm having trouble with equilibrium errors in MarvinSketch Version 5.6.0.0. I can only seem to put one arrow per page and the equilibrium arrow adds all sorts of addition signs all over my project. I'm not having a problem with the single arrow and renosance arrow, just the equilibrium arrow. The help directory was of no use. Help would be appreciated.

David Eckert

Equilibrium arrow is a reaction arrow type, and since MarvinSketch currently can handle only single step reaction, it does not allow to place more then one. The plus signs appear because the reaction automatically recognizes the structures as starting materials or products on its left and right side, and as agent above or under it.

A potential workaround is to use graphical arrows instead, but since there is no graphical equilibrium arrow, you have to create it yourself from single arrows first, and then copy/paste wherever you want it. (See the attached file.)

Would it be possible to include a graphical equilibrium arrow in a future version of MarvinSketch?

I use MarvinSketch for organic reactions that have more than one step in it. It is used by students and I've been asked several times how they can do those arrows.

Your workaround is good, but students tend to other programs which have this arrow available instead of making it out of a line which is time-consuming if one has to draw more than a handfull of reactions. If one has to use this arrow on a daily basis it would be convenient to have it in the graphical arrow menu.

We are considering adding this feature as further development. Until then, could you use the attached equilibrium arrow (equilibrium_arrow.mrv) (although I know it is not easy to adjust)?

Best Regards,

Efi Hoffmann 

Of course, I added it to the templates to make it easier to use. Thank you!

Hi,

to emphasize the importance of this request I will add here a screenshot of a tautomeric equilibrium (produced using another chemical software). The reaction scheme shows the difference of mesomerism (resonance) and reaction equilibriums. So we need to have both arrow types, and both in graphics.

And it should be not so difficult to add this little graphic equilibrium arrow to the menu at the left side of MarvinSketch. And please in this way as shown in the screenshot.

Best regards, Hans-Ulrich

Hi,

I must add here one post more: Using MarvinSketch I was not able to build the Amide-Imidic-Acid equilibrium shown one post before. Inserting the first resonance arrow produces immediately the two + signs, see attached screen shot. And then, there was no way to insert the equilibrium arrow and the second resonance arrow. The two plus signs are inacceptable.

And drawing first the equilibrium arrow in the middle produces two + signs at left and right. And once more I found no possibility to change this.

In principle this topic here is a continuation of my very old topic with the title

Resonance Arrows and Reaction Arrows are different things.

This topic finished with the discussion there might be users who use the resonance arrows for reactions, and so the resonance arrow was not moved to the graphical arrow group.

At the end of this topic I suggested to change the arrow menu at the left side and to shift the resonance arrow to the graphical group. It should be deleted from the reaction group.

In the next post I will show once more the arrow menu I suggested in the topic mentioned above.

Best regards, Hans-Ulrich

Hi,

and now the suggestion for an improved arrow menu, the new graphical equilibrium arrow and the shift of the resonance arrow to the graphics group:

1) The resonance arrow is shifted to the graphics group. For users who have used this arrow for reactions and have stored this as "RESONANCE" in mrv-files, now loading these files should be interpreted as an equilibrium arrow. So the new graphical resonance arrow should have a new name in the mrv-file, f.e. "GRAPHRESONANCE" or so.

2) In the graphical Arrows group there is a new option "Graph. Equilibrium Arrow" or so. To remember: This is the original title of this topic here.

Please do not split this in two menus. To have it in one menu gives better information about the differences.

And: And as mentioned in an earlier post here, these corrections are essential for using Marvin in education !

Best regards, Hans-Ulrich

Or we can keep the original resonance arrow and add a graphical resonanace arrow ( besides the graphical equilibrium arrow.)

Hi Efi,

this is a good way to solve the problems and to use correct nomenclature.

And I suggest to change the arrow menu as shown in the attached new screenshot.

Best regards, Hans-Ulrich

Mon Apr 16, 2012, HU: There is an optimized new version in the following topic:

Multi Retrosynthetic arrow

Thank you for your suggestions. We will notify you when this feature is ready,

Would it be possible to have the equilibrium arrow in the version available in april?

It would greatly help in teaching students in low semesters in a course about MarvinSketch/View/Space that starts in april.

I have sent you an email.