3D structure export to Excel

User 169b52bbd8

03-08-2008 03:59:00

Dear IJC gurus,

I have been working with some 3D structures SDF files in IJC. When I view the structures in IJC they are shown in 3D, which is nice, but not really what I want - so I set the display widget to show them as 2D structures. However, when I export them to Excel the structures are exported as 3D images which, again, is not really what I am after.

Is it possible to force the image format in the Excel file to be 2D? If not, this would be a useful feature. It would make the most sense to me if the Excel image format matched the IJC display format.



ChemAxon fa971619eb

04-08-2008 08:08:02

Export currently works on the raw (unformatted) data, so as to ensure that there is no loss of information.

We recognise that there is also a need to be able to specify formatting for the data during export, and plan to add this, but currently this is not possible.

As a work around you could export initially to a structure file format (e.g SDF) and then re-import that data, converting the structures to 2D when importing, and then export those 2D stuctures to Excel, but obviously this is not ideal as it involves extra steps.


User 9dface4c6c

12-08-2008 14:48:15

I also experienced related problems: if you used 3D sdf file to construct a database and select the display widget to show them as 2D structures, when double click a cell with structure, it shows in 3D.

ChemAxon fa971619eb

12-08-2008 14:55:09

Yes, this is correct. We ensure that it is always the original structure that is edited, not one that has been formatted for display.

So in this case it is the 3D version that is edited.


ChemAxon fa971619eb

14-08-2008 08:25:11

I should have added that when you edit the structure and its in 3D it is very simple to convert to 2D if that's what you require. Use the Clean 2D option from the Structure menu in MarvinSketch.


User 9dface4c6c

14-08-2008 12:09:42


Clean 2D option from the Structure menu in MarvinSketch freezes the program. I tried it three times and it happens every time.

I had to kill the program in task manager.

ChemAxon fa971619eb

14-08-2008 12:48:48

Thanks for the report. I can confirm this. It seems to happen the second time you run clean2D.

We will look into it and fix.



User fdee5ee126

12-11-2009 09:24:38

Hi there, I recently had exactly this Problem.

I wonder if this is now solved and I just cant find the right menu?

ChemAxon fa971619eb

12-11-2009 12:51:49

There are two different problems described in this topic, and its not clear which one you were referring to.

1. export to Excel exports structures in their original format

This is still the case. We do plan to provide more flexible formatting options for export in the fututre.

2. Clean 2D freezes when use a second time.

This problem is fixed.