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Multi Retrosynthetic arrow
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Romualdas

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Link to postPosted: Fri Apr 06, 2012 10:05 amPost subject: Multi Retrosynthetic arrow Reply with quote

Hi,

I wish to draw a scheme with multiple retrosynthetic arrows. Could some one help me to construct a multi step retrosynthesis reaction scheme?

Thanks

 

István
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Link to postPosted: Fri Apr 06, 2012 11:59 amPost subject: Reply with quote

Hi,

in the current Marvin version we do not support to draw multi step reactions, and since the Retroshyntetic arrow is a reaction arrow not a graphical one you can not do that currently.

This was the bad news, the good news is that we are working on to add various graphical arrows to marvin to at least support the drawing of multi step reactions, without complex computations. The Retrosynthetic  arrows is one of the developing arrow types, so in 5.10 you will be able to draw such reaction schemes.

I hope this can be suitable for you, this is the closest point that we can currently promise.

5.10 is being released in June according to our current schedule.

Thank you for your patience.

Regards,
Istvan

Hans-Ulrich

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Link to postPosted: Fri Apr 13, 2012 10:23 amPost subject: Reply with quote

Hi, first I have a question here:

Does that mean, one more graphical arrow type will be added to the arrows menu ?

I refer to the actual suggestions in the topic

Equilibrium Arrow Problems

 

And a second reference concerning the arrow problems:

Resonance Arrows and Reaction Arrows are different things.

 

Regards, Hans-Ulrich

Eufrozina
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Link to postPosted: Sun Apr 15, 2012 9:32 amPost subject: Reply with quote

 

The following new arrow types will be added for 5.10:

-graphical equilibrium arrow;
-graphical retrosynthetic arrow;
-curved arrow;
-dashed arrow;
-crossed arrow.

Best Regards,

Efi

Hans-Ulrich

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Link to postPosted: Mon Apr 16, 2012 10:24 amPost subject: Reply with quote

Hi Marvin developer, so I must continue our long discussion here:

First a documentation of the present status, Marvin 5.9.2.

In the first attached screenshot you see the inacceptable usage of the "Resonance Arrow". We had a very long discussion about this subject, I must repeat the link here:

 Resonance Arrows and Reaction Arrows are different things.

And at the end there were these sentences of Akos:

"Now I'm seriously considering your suggestion. Since this topic opened there was no any objection here, so this might mean that not too many users use resonance arrows in reactions... on the other hand, I need more feedback to be sure, so I will ask some users who frequently use reactions about their opinion.

In the second attached image there are the two (!) menus having arrow options. There is no need to have two menus. The arrows should have their own menu and only one.

In the next post, I will attach an optimized suggestion how to manage the arrow menues. It's important for the usage of Marvin in education to have a consistent and intuitive GUI.

Best Regards, Hans-Ulrich

The attached image of arrow menus has been deleted. April 23, 2012, HUW.




 Filename: Napthtalin-Resonance-Crash.png    Filesize: 44.99 KB    Viewed: 22167 Time(s)
 Description:  Resonance arrow problem
Napthtalin-Resonance-Crash.png


Last edited by Hans-Ulrich on Mon Apr 23, 2012 8:54 am; edited 1 time in total
Hans-Ulrich

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Link to postPosted: Mon Apr 16, 2012 10:49 amPost subject: Reply with quote

Hi, now attached an optimized version of the new Arrow menu.

The options mentioned two posts before are included.

Please, only one Arrow menu, to have two is rather confusing.

And please delete the wrong resonance arrow from the reaction arrow part. The option for this two headed arrow should only be in the graphical part.

Best regards, Hans-Ulrich

Attached arrow menu image has been deleted. April 23, 2012, HUW.



Last edited by Hans-Ulrich on Mon Apr 23, 2012 8:51 am; edited 1 time in total
Eufrozina
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Link to postPosted: Mon Apr 16, 2012 9:19 pmPost subject: Reply with quote

Thank you for your suggestion, we will consider it as a possible solution of organizing the arrows, however, I think we should keep the original retrosynthetic arrow for the users who got familiar with it.

Best Regards,

Efi

Hans-Ulrich

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Link to postPosted: Mon Apr 16, 2012 9:27 pmPost subject: Reply with quote

Hi Efi, sorry, I don't understand.

Do you mean the retrosynthetic arrow or the resonance arrow ?

The retrosynthetic arrow is in both menu parts.

And to have the resonance arrow in the reaction part is absolutely wrong.

Best regards, Hans-Ulrich.



Last edited by Hans-Ulrich on Sun Apr 22, 2012 2:56 pm; edited 1 time in total
Eufrozina
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Link to postPosted: Mon Apr 16, 2012 10:21 pmPost subject: Reply with quote

Oh. Sorry I meant resonance arrow. And I can see your point that: Resonance Arrows and Reaction Arrows are different things, however, I also have to consider the other users' needs who have been using resonance arrow from years.  All I can imagine now to separate the resonance arrow from the reaction arrows.




 Filename: arrows_panel2.png    Filesize: 16.33 KB    Viewed: 22127 Time(s)
 Description:  
arrows_panel2.png
Hans-Ulrich

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Link to postPosted: Tue Apr 17, 2012 9:15 amPost subject: Reply with quote

Hi Efi, I cannot agree, but let's make a compromise:

I have attached an arrow menu version 8 and I think, two points are important.

1) Now the "Two-headed Arrow" in the upper "Reaction Arrows" menu part has nothing to do with resonance. This "Reaction Arrows" type produces real reactions, just as shown in a post before in the "Naphthalin-Resonance-Crash" image. So the word "Resonance" is not acceptable in the upper "Reaction Arrows" menu part.

2) The original theme of this topic concerned the same problem. There was no possibility to construct a multi step retrosynthesis reaction scheme. And the same problem is for pi-systems having many resonance formulas,  e.g. the heptamethincyanin cation N\C=C\C=C\C=C\C=[NH2+]. Here there are at least 6 resonance formulas.

The Resonance Arrow has to be only in the Graphical Arrows menu section.

We need to have a correct MarvinSketch version for education in our chemistry campus. And we need it as fast as possible. Please manage the arrows toolbar just as in the attached version 8.

I have also added the "curved - dashed - crossed arrow" options you mentioned in the posts before. I think these should also be in this menu.

Best regards, Hans-Ulrich

Attached menu version 8 image has been deleted. April 23, 2012, HUW.



Last edited by Hans-Ulrich on Mon Apr 23, 2012 8:48 am; edited 1 time in total
Hans-Ulrich

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Link to postPosted: Sun Apr 22, 2012 3:20 pmPost subject: Reply with quote

Hi Efi,

I refer to the topic

Strange behaviour of pdf and color: monochrome ?

There you are announcing a new release Marvin 5.9.3 for the next week.

Will the arrow problems of this topic and the

 Equilibrium Arrow Problems

be solved in this new release ?

We really need it to start the next student course the next week.

Best regards, Hans-Ulrich

Eufrozina
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Link to postPosted: Sun Apr 22, 2012 8:11 pmPost subject: Reply with quote

Dear Hans-Urlich,

Unfortunately, we are not ready with the new arrows yet. Besides that, considering your suggestions and other user needs, we decided to separate the original resonance arrow from the reaction arrows group. It means the users will be able to  add and delete it by customization. To do this a major rewriting  of this part of the code is needed.
The task "Strange behaviour of pdf and color: monochrome ?" is a different issue, this bug could be fixed easily. There will be an 5.9.3 release due to other reasons, it was reasonable to  add this bugfix too. If we have a stable test version including the arrows, I can send it to you.

Best Regards,

Efi

Hans-Ulrich

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Link to postPosted: Mon Apr 23, 2012 8:46 amPost subject: Reply with quote

Dear Efi, let's make a priority list:

For our student courses producing organic synthesis protocols we need to have:

1) Graphical equilibrium arrow

2) Graphical retrosynthetic arrow

This is essential and I refer once more the following topic at the end:

Equilibrium Arrow Problems

And I think, this is only adding these two graphical arrow types more. I think it could be done soon.

3) The renaming of the already present <-> arrow types, as shown in the attached version 9, is a correction of the notation of this menu. These wrong notations are not a hindrance and we could alert the students about it.

As already asked in an other topic of me: May I have a look in the MarvinSketch code, as a long time JAVA programmer

Best regards, Hans-Ulrich

PS: I will delete my menu images in the earlier posts in this topic.




 Filename: ArrowMenu9.png    Filesize: 19.02 KB    Viewed: 22008 Time(s)
 Description:  Arrow Menu version 9
ArrowMenu9.png
Eufrozina
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Link to postPosted: Wed Apr 25, 2012 9:21 amPost subject: Reply with quote

Dear Hans-Urlich,

I understand your priorities. And we can make the changes you suggested on the arrow panel, however, the file representation  of the arrows will not be changed.

Best Regards,

Efi

Hans-Ulrich

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Link to postPosted: Wed Apr 25, 2012 1:42 pmPost subject: Reply with quote

Dear Efi, that's a really good decision !

The arrow type in the mrv-file  <reaction><arrow type="RESONANCE" is not to be seen by GUI users and so we can use MarvinSketch for student courses without problems. And users of the command line Marvin programs still have their familiar procedures they are using long time.

And now we are looking for the two new Graphical Arrow types

1) Graphical retrosynthetic arrow 

2) Graphical equilibrium arrow

Best regards, Hans-Ulrich


Eufrozina
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Link to postPosted: Thu Apr 26, 2012 4:28 pmPost subject: Reply with quote

Hi Hans-Urlich,

I have just sent you a mail.

Best Regards,

Efi

Hans-Ulrich

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Link to postPosted: Wed Jun 13, 2012 7:20 pmPost subject: Reply with quote

Hi Efi,

having now 5.10.0 these old problems have gone and the bugs are fixed, see attached screenshot.

Thank you.

Best regards, Hans-Ulrich




 Filename: ArrowMenu11.png    Filesize: 51.51 KB    Viewed: 21547 Time(s)
 Description:  Equilibrium and Resonance Arrows
ArrowMenu11.png
Eufrozina
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Link to postPosted: Wed Jun 13, 2012 7:45 pmPost subject: Reply with quote

You are welcome.  Thank you for the screenshot, it is always nice to see that it works!

Best Regards,

Efi

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