1. From MarvinSketch to Blender

This tutorial guides you through the process of converting a molecule drawn in MarvinSketch into a format usable in Blender, using Open Babel and Gaussian2Blender.

Requisites

Before starting, make sure you have the following installed:

  • Open Babel A chemical toolbox designed to speak the many languages of chemical data. Documentation: Open Babel 3.1.1

  • First Generation Marvin Software Includes MarvinSketch and MarvinView.

Step 1: Open MarvinView

  1. Launch MarvinView.

  2. Navigate to Edit > Structure to open a MarvinSketch window.

  3. In the MarvinSketch window: - Draw your molecule. - Go to Structure > Add > Explicit H Atoms to add all hydrogen atoms. - Go to Structure > Clean3D > Clean in 3D to generate 3D coordinates.

  4. Copy the molecule: - Go to Edit > Copy As … - Select .mol format.

Step 2: Convert to .mol2 with Open Babel

  1. Open Open Babel.

  2. Use the GUI or command line to convert the .mol file to .mol2 format.

    Example command:

    obabel input.mol -O output.mol2

Step 3: Use TheorChem2Blender

  1. Open TheorChem2Blender.

2. Follow the tool’s procedure to convert the .mol2 file into the desired format for Blender (e.g., .obj, .fbx, etc.). NOTE: For more information on the steps for using TheorChem2Blender, see tutorials 3 through 10 in this page.

Next: (2) From Molecular Dynamics to Blender (General)

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