How to save molecules into grid rather than free floating

User b85e2e3247

24-06-2011 19:29:32

I have MarvinView Files and the appear as shown below, but I need them to be saved in a format where they are organized into a numbered grid (also shown below) so that when i import with JChem for excell they import as one molecule per cell rather than a block of many molecules in 1 cell


Thank you,


ChemAxon bd13b5bd77

25-06-2011 07:09:10


does MV have  a feature to display the multi-component molecule in separate cells?


ChemAxon 990acf0dec

27-06-2011 08:49:15

Hi Graham,

If the molecules in an SDFile appears in a single cell, than it means that there is only a single molecule record. So it is not about the format or the viewer; you need a tool that export each molecules to a separate record. Currently neither Marvin nor Molconvert can do that :(

Best regards,


ChemAxon bd13b5bd77

27-06-2011 09:01:39

Hi Graham,


are you sure that JChemExcel imports that SDF fragement/cell? So in different way of how Marvin View does it?


If it does, please use JChemExcel for defragmenting the molecule, I mean import the SDF into JChemExcel, and afterwards export it into SDF again. I am very curious about if the re-exported stuff looks in different if you open it in Marvin View again?

If the problematical file is not confidential, could you please send us for reproducing th issue?

The file can be sent dirrectly to us, not via the forum.

Akos Papp <[email protected]> and [email protected] <[email protected]>



User 421219f4d4

19-11-2011 09:57:55

I also have a file from an user.  The file has multiple structres drawn in the chemdraw, is there a way to store them as seperate entities using chemaxon tools?

I have attached the file for reference.

ChemAxon bd13b5bd77

21-11-2011 07:31:06

Hi Surojit,

Checked your file and the problem looks the same as you might have read in the current forum.
Your file contains 1 molecule with 4 different structures, it is handled as 1 composite molecule in 1 record.

I think what you should do is to try to defragment it by using API or Fragmenter.


this feature could go into Marvin View as well. Your opinion?

We try to implement this feature in one of the next upcoming releases in JChemExcel too,




User 421219f4d4

21-11-2011 08:44:19

Thanks Viktor, I used fragmenter via KNIME and could split my molecule. 

Wondering if there is a way which can help me to directly export these molecules into a database, so that they are readily available in IJC. 

ChemAxon bd13b5bd77

21-11-2011 09:11:26


We implement this defragmenting stuff in JChemExcel anyway, we try to schedule it for 5.8 JC4XL release.

Yes, IJC is good to store molecules, and the JChem Manager is also a good tool for that.

To check how your database state looks like IJC, JC4XL can be used for retireval part.