Jmol

Blender Tutorial Using the Free Program Jmol to Look at Chemical Structures and Exporting to Blender

• Report rights infringement
• published: 02 Apr 2016
• views: 437

NOTE: Blender version 2.77 onwards has improved X3D file import and does not have the problem described in the tutorial. This tutorial shows how to download Jmol, a free 3D chemical structures application and it shows the basics of how to use it. This tutorial shows how to access small and large molecules in Jmol and how to export them in a format that can be imported into Blender. It also shows how to refine the imported models in Blender. Additional material: The tutorial has additional material that shows how to edit a molecule in Jmol and it takes a quick look inside an X3D file in a text editor. Websites - Jmol website http://www.jmol.org Jmol uses the following Internet resources for small molecules NCI/CADD Chemical Identifier Resolver http://cactus.nci.nih.gov/chemical/structure PubChem Search http://pubchem.ncbi.nlm.nih.gov/search/ My chemistry page http://blender.freemovies.co.uk/chemistry/ The steps are - Goto Jmol site and download zip file Extract the Jmol folder to a suitable location Go into the Jmol folder and double click Jmol.bat (or Jmol.jar) NOTE: You MUST have Java runtime installed Use File menu, Get Mol to get small molecules by name Use File menu, Get PDB to get large molecules using their PDB Ids To export a molecule as as x3d file, right click in the view area, File, Export, Export X3D, give the file a meaningful name and save in a suitable folder To Import into Blender Delete the cube File menu, Import, X3D, goto folder, select file, click Import Using the Outliner window, select the spheres that are used at the ends of the bonds and delete them The cylinders that represent the hydrogen to carbon bonds are a set of linked duplicates that can only be linked to one material, select a hydrogen bond, in the Object menu, Make Single User, Object & Data and click Selected Objects Click the Object Properties button to show the new underlying mesh Select each hydrogen bond, click the Browse Mesh Data button and link them all to the same underlying mesh Which a hydrogen bond selected, click the Material Button, click the Browse Material button and set the material to hydrogen To make the molecule into a single object, Select menu, Select All by Type, Mesh and click the Join button In the Object menu, Transform, Origin to Geometry Set Shading to Smooth and in the Object properties give the model a meaningful name, ethene All files can be downloaded from my website - http://blender.freemovies.co.uk