NBCR Summer Training 2018

This tutorial will start with an introduction of the mesoscale and the different tools we developed in the MGL lab, as well as an overview of the tutorial. The tutorial will be conducted by: Brett Barbaro, Ludovic Autin, Adam Gardner, and Andrew Jewett.

Initial Preparation

- you need a recent browser like Firefox or Chrome

- you need Blender plus the plugins

Download the bundle for your OS :

Bundle for Windows 64bits

Note for Windows User:

    if the plugin doesnt start, try to install the visual C++ redistributable for vs2015  https://www.microsoft.com/en-us/download/details.aspx?id=48145

Bundle for MAC OS 64bits

Note for Mac user: 

    Unzip the package in your user>Downloads folder.

    We provide an alias to run Blender in the terminal, so do not double-click blender.app - double-click "run_blender.command" instead.

    If it doesn't work, open the "run_blender.command" file in a text editor and replace the path to Blender by the one you have download Blender into.

Bundle for Linux 64bits

Note for Linux user: 

    install/unzip in your user folder

    before running ./blender you need to update the LD_LIBRARY_PATH to point to the MGLToolsPckgs. e.g export LD_LIBRARY_PATH=/pathtoblender/MGLToolspckgs:$LD_LIBRARY_PATH;./blender

We recommend user to check the blender reference manual and the getting started section: https://docs.blender.org/manual/en/dev/.

Recipe Preparation - Mesoscope


Go to : https://mesoscope.scripps.edu/beta/

If you have problem with webGL try to enable it (e.g. see here )

Preparing the recipe hierarchy

Note: If you changed the nodes color, you can view it in the canvas by changing the pull-down color to "color"

At this point you should have the following visual (the locations of your ingredients may differ depending on where you dropped them, but that doesn't matter):

Gathering the structural and geometrical data for each ingredient

Elongation Factor



Final Check

Export to cellPACK

The recipe is ready to be exported! In the gray command bar at the top, click:

Export->cellPACK recipe

Export->cellPACK-gpu recipe

This should save/download both files in your user Downloads folder. You can also find these recipes here:



Building the model - cellPACK-Blender

Step 1 Set Up

In the Viewport you will see a cube and some other stuff. In the Outliner you will see a "Cube" object and some other stuff corresponding to the things in the Viewport. The "other stuff" is not important for this tutorial - just ignore it.

Step 2 Load a recipe in autoPACK

Step 3 Build the model


Building the model - real-time cellPACK-gpu prototype (only windows)

- download cellPACK-gpu for windows.

- unzip and run cellPACKgpu.exe

- browse to load the recipe you exported from mesoscope (myrecipe_serialized.json)

- interface help 

Simulation of a model - MOLTEMPLATE-LAMMPS

LAMMPS is an extremely flexible and customizable molecular dynamics engine. Moltemplate is a general cross-platform text-based molecule builder for LAMMPS. Moltemplate was designed for inventing new kinds of complex coarse-grained toy models of molecules, molecular machines, and assemblies. However it is well suited for preparing realistic all-atom simulations as well. It supports a wide variety of existing force fields including: OPLS, AMBER(GAFF,GAFF2), COMPASS, MARTINI, SDK, LOPLS(2015), EFF, and TraPPE(1998), however it can be used to build molecules using any of the force fields (and atom styles ) available in LAMMPS, including new force fields created by modifying the LAMMPS source code. Molecules can be copied, combined, and linked together as building-blocks to define new molecules (hierarchically). Once built, individual molecules and subunits can be customized (atoms, bonds, and subunits can be moved and deleted). Moltemplate is currently interoperable with: VMD, PACKMOL, cellPACK, OVITO, and the ATB molecule database.

Cellpack2moltemplate has been developed for the purpose of simulating cellPACK models with an accurate simulation engine (LAMMPS). 

We will demonstrate the current version (which is still in development) applied to a simple cellPACK model, as well as how to playback the simulation in the cellVIEW/cellPACK-gpu rendering engine. As a quick reference note, the pipeline is:

- Mesoscope -> recipe -> cellPACK -> model -> cellpack2moltemplate -> system -> moltemplate -> input -> LAMMPS

In the future cellpack2moltemplate will be directly integrated in cellPACK. 

Andrew Jewett will then show some simulations done with Moltemplate and LAMMPS.

Painting a model - cellPAINT

CellPAINT is an evolving effort to bring mesoscale biology to the general public. Our initial version of cellPAINT was developed in 2D, and was intended to give a better understanding of the structural biology of the HIV virus. We have continued the development of cellPAINT as a 3D painting tool, using proteins as a palette. We will demonstrate the latest version of cellPAINT using an introductory recipe and a more advanced one.

To use your recipe in cellPAINT, in the sprite option generate a sprite with NGL or Illustrate. Then save cellPAINT recipe and sprites.

Download the latest version of cellPAINT2D and browse to the tutorial page.

Try the latest cellPAINT