Problems saving reaction to a .mol-file from MarvinSketch

I am seeing a lot of strange problems with saving a reaction to a .mol-file from MarvinSketch. It is not that consistent, and doesn't always happen, but it is fairly commonly occurring for me.

When adding a reaction arrow and then using File → Save as, .mol-files (MDL Molfiles) are often removed from the list of choosable file formats, but not always. However removing the reaction arrow and then saving as a .mol-file and then adding the reaction arrow again usually works, and .mol-file is after that choosable in the save-as-menu.
And I have seen some weird behavior when opening a empty .mol-file and then adding a reaction arrow and then saving, where I have multiple times gotten a .mrv-file saved with a .mol ending. So that applications that can't handle .mrv-files cannot open the file.

I have tried this in versions 6.1 and 14.9.1 under both Windows and Linux, with more or less the same behavior in all of them.

Does anyone know of a solution or a good workaround?

Is this a bug in MarvinSketch? Is there a better place than the forums to write bug-reports to for normal users?

Dear ealmen,

In Marvin if there is a reaction on the canvas the MDL .rxn format  (out of MDL formats) is used to save the structure. For reactions there should be no option for MDL .mol file on the save dialog, but if there is an option for it the save process will override it and saves the structure as an MDL .rxn file.

I hope this helped,
István 

istvanori wrote:

Dear ealmen, In Marvin if there is a reaction on the canvas the MDL .rxn format  (out of MDL formats) is used to save the structure. For reactions there should be no option for MDL .mol file on the save dialog, but if there is an option for it the save process will override it and saves the structure as an MDL .rxn file. I hope this helped, István

Thank you for clearing up about MDL .rxn-files. That certainly makes things clearer for me.

The problem I am having is that I have another application that generates mol-files, sometimes without reactions and sometimes with, but it always uses .mol as file ending, but it uses rxn-format but saved with a .mol ending when using reactions.

Now when opening a mol-file in MarvinSketch and adding a reaction arrow and saving MarvinSketch saves using .mrv-format but to the .mol-file. And then when I try to import the modified .mol-file the application gives an error because it isn't compatible with the mrv-format.

I have seen many applications treat mol- and rxn-files as more or less the same with not so much care taken to force proper file names.
And after digging a bit ChemAxon sometimes does the same. MarvinSketch version 5.6.0 seems save as rxn-format but to a .mol name when adding a reaction arrow. And molconvert uses the mol-format setting to use mol if not a reaction and rxn-format if it is a reaction in even the newest versions of MarvinBeans.
I could downgrade to 5.6.0 for this problem, but I unfortunately have another application that uses MarvinSketch, and is not compatible with version that old.


Was it a deliberate switch to defaulting to mrv-format when it can't save the document as a mol-file?
I realize that there isn't a fully correct behavior here, and maybe a error message explaining that mol-files can't properly contain reactions would be better. But for the best compatibility using rxn-format instead of mrv-format would be better in my eyes.

Are there any settings for this? Would it be difficult to switch back to using rxn-format when saving reactions to mol-files instead of mrv-format in future versions of MarvinSketch?

Dear Ealmen!

   We need to discuss what to do with this issue, since it is clearly gives a faulty behavior but it is not clear which way should we heal it. Thank you very much for your report, we will inform you here if any fix is available in any of our future releases.

Regards:
Balázs