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How to generate 3D structures with Marvin Molconverter node?

Member for

4 years 6 months gcincilla

Hi Marvin lovers,

I'm trying to use Marvin Molconverter node to convert smiles to 3D structures. Googling around I found that in the batch version of molconverter this is done using the “-3” option, and “-3:[prehydrogenize]” to output hydrogen atoms explicitly.

Nevertheless when I add these options in the to the "Output Options" box, the Molconverter node triggers the warning “Unknown option(s)”.

Please, can anybody help in this?


Fri, 09/30/2016 - 06:57

Member for

10 years 4 months


Hi Gio,

Unfortunately, the node doesn't support the option.
The node supports only the Basic export options and specified options for each format.

It's only available in comercial products now.


Fri, 09/30/2016 - 09:07

Member for

4 years 6 months


OK Tohshima, thanks for the info.

Wed, 12/07/2016 - 07:42

Member for

10 years 4 months


New Free Marvin Nodes has the following enhancment.

   Add 'Remove small fragments' options.
   Add 'Cleaning' options.