Problem with Editing Structure with Brackets and Multiplier

User 70a655032c

25-02-2010 20:30:36

When I try to edit the a structure with brackets and multipliers in ChemDraw and then save it back to the spreadsheet, the cell is cleared.

The attached spread sheet contains a compound with bracketted Na ions. If you attempt to edit this structure with ChemDraw, (Just move the bracket and then save), the cell is cleared. (the formula is actually deleted).

 Seems to work with everything except bracketted fragments. If I place 3 NA+ ions in the editor, it's fine.

ChemAxon 0e37943a96

26-02-2010 10:01:12


we will have a look at the problem. In this version we use MOL file with ChemDraw, so it has a few limitations.

In the next version we will switch to CDX import and export.


PS: I will give you some more details in E-Mail.

ChemAxon bd13b5bd77

26-02-2010 16:31:35

Dear Charles,

thanks for the test, and steps to reproduce the issue.

The cell gets cleared an exception caused by our IO module and producing NO Sketch, which fires deletion in the cell. 

For the first sight the situation might seem to be an JChem4XL bug BUT after checking the situation on different environments:

- JChem4XL and ChemDraw 11.0 the issue is reproducible.

- JChem4XL and ChemDraw 7.0 the issue is NOT reproducible. In this case the content of the cell is kept, however after the bracket the multiplyer value (3) is removed. But any change I draw in will be reflected in the cell (e.g. adding an acethilen, or whatever...)

To me the issue seems to me ChemDraw version dependent.
The output different ChemDraw versions produce(MDL MOL) is different and it is handled differently by out JChem/Marvin IO module.  

The issue is forwarded to our JChem/Mavin team for further checking as a high prority task.






ChemAxon bd13b5bd77

26-02-2010 17:22:21

After further checking I made with Symyx Draw 3.2 the molecule is not the same, the index number changed from 3 to 0.

I think the MOL file ChemDraw writes out is INCORRECT.

Our JChem/Marvin team also checked the issue, and they reported that ChemDraw output produces an incorrect MOL file format in which the molecules are not included in bracket physically. The Na itslef is not written to the MOL file correctly (it should have been written 3 times there) so that way the empty SGroup cannot be imported, the ion is absolutely disconnected from the bracket.

The conclusion is that this input for JChem/Marvin and other editors is invalid!

Please report this problem to Cambridge Soft anyway they should fix their MDLCT/MOL export via files as well as OLE interface.

For the time being please continue drawing brackets with Marvin .NET, in the next version we try to come out with CDX import/export which is hopefully available via ChemDraw OLE interface and compatible more with our module importer,

producing better compatibility between the two product families (ChemDraw and Marvin).


ChemAxon bd13b5bd77

10-03-2010 23:32:43

Based on ChemDraw help you should find other alternatives to draw bracket and stochiometric expressions like this.

please see the attachment.

Marvin .NET editor supports such the drawing format. If you would like to have the same feature in ChemDraw please contact the vendor.

Smaller issue we found in Marvin re MOL file handling, it is a kind of sensitivity against extra spaces the ChemDraw exports. This issue will be fixed in Jchem/Marvin lib 5.3.2 early April.