Visualizing 3D structures as holograms - Using MergeCube

1. Visualizing 3D structures as holograms


1. PyMOL (or Chimera)- for structure preparation

2. Merge Cube - Object Viewer - app for augmented reality

3. Merge Cube - device for augmented reality

4. Miniverse - online account

1.1. Structure preparation

Set the desired color, style and other visualization options in your favorite visualization tool. In this example, we use a ribbon style for a protein molecule imported from PDB

into PyMOL (or Chimera- see alternate instructions 2a.).

1.2. COLLADA export

1. 2a. Export the image from PyMOL in a COLLADA format, using the File - Export Image As - COLLADA… menu option in PyMOL.  Save this with a “.dae” file extension.


1. 2b. If you prefer to use Chimera instead of PyMol, use File>>Export Scene.  Set File type to “COLLADA .dae”, give a file name and click Save.




For .dae files saved in Chimera, you must open the file in a text editor and add the following line as the first line, exactly as shown, then save the edited file:


<?xml version=”1.0” encoding=”UTF-8”?>

1.3. Upload structure to Miniverse

  • In your miniverse account, choose the “My Objects” option, Click “Add New” button and then Click “Choose a file” button, to navigate to your folder containing the .dae file you saved.
  • If you do not have one, you can create a new miniverse account at ; https://miniverse.io
  • A successful upload will give you a unique code that you could use to load your structure in object viewer app



1.4. Load Structure in Object Viewer

  • Start the Object Viewer app in your mobile phone and choose the “Phone Mode”.
  • Enter your object code “MYL6DD” and click “Load” button.
  • Once loaded, hold the phone in one hand, hold the merge cube in another hand and move the merge cube right before your phone, to see the hologram of the structure in your phone screen



1.5. Structure visualization

  • You can change the size of the object to get it how you want for the picture by tapping in the box where the object appears, then click Edit in the menu that appears.  
  • Click Scale in the Edit menu, and resize by moving your finger up and down.  
  • When finished, click Done, then again click Done, and finally click outside the object to remove the menu.

Reference: https://www.macinchem.org/reviews/3D/augmented.php

1.6.  Using structures from Jmol applications

Some online applications use Jmol (or JSmol) to display molecular structures.   Examples are PyCoMFA and ZINCPharmer. You can export these images into 3D formats as follows:


1.6.1  Control-click in the graphics window and choose File>>Export>>Export X3D 3D model



Enter a filename and click OK (you may have to click OK twice).


1.6.2  Launch MeshLab and open the .x3d file you just created:

File>>Import Mesh

1.6.3  Look at the bottom of the screen.  If the number of vertices is more than 250,000 you should simplify (decimate) the mesh:o

Filters>>Remeshing, Simplification and Reconstruction>>Quadric Edge Collapse Decimation

Set “Target number of faces” to 250000 and click Apply.

1.6.4  Export the mesh as a .dae file.

File>>Export Mesh As…

Choose “Collada File Format (*.dae)” as the file format, give the new file a name, and click Save.


1.6.5  Upload the file to Miniverse and view it with a Merge Cube as in steps 18.3 - 18.5 above.