Hydrogen representation and storage to sdf format

User 6b694845c2

03-08-2015 10:34:18

Dear ChemAxon,

In JChem for Excel I have set the options menu for Hydrogens as follow



My question is why the Hydrogens are not saved in the sdf file format.

Thank you!


ChemAxon 044c6721bc

03-08-2015 12:57:12

I've moved your question to the appropriate forum. My colleagues will answer you soon.


ChemAxon a3dda216df

04-08-2015 13:58:59

Hi Terry,

Please, let me know the followings:

-which version of JChem for Excel are you using: 15.4.13?

-what is you MS Office version: Office 2010, 64bit in Windows7?

Did you convert the SMILES string exactly the same way as previously?

Please, check if the option in JChem for Excel: CD Clean During String Conversion is set to True, and what is the status of the option: "Structure Display/Preferences-Bonds/Aromatic Bonds as Discrete Double Bonds"

As far as I see from the screenshots, the first 2 structures have 3D coordinates, the second have only 2D.

The hydrogens should be saved in the sdfile when exporting, but depending on the display options, they are not visible. Please try the following:

1. double-click on the structure: Marvin editor opens.

2. In Marvin, in Structure menu, press Add/Explicit Hydrogens: now all the hydrogens should be displayed in Marvin.

3. Press Ctrl+A, then Ctrl+C, close Marvin editor.

4. Go to an Excel cell and press Ctrl+V. Please, check if the hydrogens are now all visible.

Hope this helps, but let me know, if you have further questions.


User 6b694845c2

04-08-2015 15:25:31

Dear Anna,

Please ignore the question's part about converting from smiles to molecular structures. I will delete it.

The version of JChem for Excel I am using is the 15.3.2300.2514 (Office 2010 in Windows 7 64bit).

It seems I have a problem with saving the structures' hydrogens into the sdf files. I will try your suggestions and let you know.

Many Thanks!