Displaying multiple molecules from a CML file

Hi,

I'm trying to import a multi-molecule file into a Marvin Sketch window that I have embedded in a browser window. I have a general understanding of how .cml files are formatted, but I'm stumped on this one. I have searched around to try to find an example of displaying multiple molecules from one .cml file, but to no avail.

I have a few questions:

-Am I correct in my understanding that MarvinSketch can only display one molecule at a time, and if it is provided with a file with multiple molecules, it treats them as the same molecule?

(I am going on what I read on this page: http://www.chemaxon.com/marvin-archive/3.5.5/marvin/chemaxon/marvin/help/sketch-basic.html)

-Unfortunately, due to my limited knowledge of chemistry, I am unable to tell whether treating 2 molecules as the same molecule would have any disasterous consequences, so please advice me on that as well.

-How exactly does one write a .cml file that contains two or more molecules? I understand there is an option called "MULTISET" for the mol parameter, but I don't really know how to use it.

(I got that information from this page: http://www.chemaxon.com/marvin-archive/3.5.7/marvin/doc/dev/sketchman.html)

 

Thank you very much!

Hi,

First of all the current documentation can be found under this page. This documentation is for the current release, the links you have linked, are in the documentation of releases that are more than five year old.

In the current versions of Marvin, there is a possibility to open multiple structures from a multimolecule file, but the save of those structures a bit tricky. You can find information on this in the current documentation here.

I can suggest that to open the structures from the file one by one, edit it, and save the changes, this is the most secure way of handling multimolecule files. You can open a structure by its ordinal, you can see the structures in the preview window of the file chooser dialog, and you can also find out the ordinal for a given structure.

I hope this helps, if you have further questions, please do not hasitate to ask.

Regards,
Istvan

Hey, thanks a lot for the information, and for giving me the current documentation.

My ultimate goal is to be able to display one or more molecules in the same window and also have electron flows between them. Do .cml files support electron flow? Or do I need to look into a different format? The key thing is that I need to document interactions between two or more molecules.

Thanks again.

Hi,

.cml does not support electron flow arrow. Can you use .mrv format?

Best Regards,

Efi

Yeah, upon further inspection I think I can use the .mrv format. I need to be able to parse the format into a database table, and it looks like the .mrv format isn't that much different from the .cml format (which I am using now). If possible, would you be able to provide me with a sample .mrv format file that contains 2 molecules with an electron flow between them?

Thank you so much for your help in this matter.

Hi,

I'm adding an .mrv file containing a reaction of 2 molecules, with electron flow between them.

Best regards,

Dora

Awesome. Thanks for posting that. I want to be able to open up .mrv like that and save them as well.

When I opened that .mrv file in MarvinSketch, then saved it (without changing it at all), the electron arrows were gone. Are there some fine details that I am missing about how Marvin exports files?

Thanks again!

Hi,

could you please write which version of Marvin do you use? Since version 5.10, disconnected molecules can be saved separately in MarvinSketch. For the documentation see:  http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#save2molformat

If you want to retain the Electron Flow arrows, you should choose the first option: "Save as a single file containing all structures together".

Best regards,

Dora

Oh, yeah, saving them all as one molecule did fix it. Are there any subtleties or ambiguities that might occur if I save all the molecules as one structure? I need to retain those electron flow arrows, but I would prefer the molecules to be saved separately if possible.

I'm using Marvin 5.10.4. I guess I should update to the newest version. Thanks for the advice.

Unfortunately, it is not possible at present to save the molecules separately and retain electron flow arrows at the same time. Currently, only saving the structures together can do this.

Best regards, 

Dora