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Hydrogen representation and storage to sdf format
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Eleftherios

Joined: 25 Mar 2015
Posts: 28

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Link to postPosted: Mon Aug 03, 2015 11:34 amPost subject: Hydrogen representation and storage to sdf format Reply with quote

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!

Terry



Last edited by Eleftherios on Tue Aug 04, 2015 4:28 pm; edited 1 time in total
Janos
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Joined: 02 May 2011
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Link to postPosted: Mon Aug 03, 2015 1:57 pmPost subject: Reply with quote

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

Janos

Anna
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Joined: 27 Feb 2012
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Link to postPosted: Tue Aug 04, 2015 2:58 pmPost subject: Reply with quote

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.

Anna

Eleftherios

Joined: 25 Mar 2015
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Link to postPosted: Tue Aug 04, 2015 4:25 pmPost subject: Reply with quote

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!

Terry

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