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BlendMol is a Blender plugin that can easily import VMD 'Visualization State' files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with a popular analysis program (VMD).

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durrantlab/blendmol

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BlendMol

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BlendMol 1.3

BlendMol 1.3 is a Blender 2.8 plugin that can easily import VMD "Visualization State" files. It interfaces directly with the VMD executable to 1) normalize the VMD camera position, 2) render molecular meshes to Blender-compatible files, 3) import those files into Blender, and 4) optimize mesh geometries as needed.

One can also work entirely within Blender, without ever opening a dedicated molecular-visualization program. If the user provides a PDB ID or a PDB file, the plugin uses VMD to automatically generate a simple, default visualization.

BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with the popular analysis program VMD. Users import into Blender the very molecular representations they set up in VMD.

The Latest Version

To view the source code of the latest version, visit https://git.durrantlab.com/jdurrant/blendmol.

Visit https://durrantlab.com/blendmol/ to:

  • read the documentation
  • suggest an improvement
  • point out a bug
  • ask a question about usage

Authors and Contacts

BlendMol was created by Jacob Durrant (durrantj@pitt.edu).

Installation

Quick Start

BlendMol installation within Blender is the same as with any Blender plugin:

  1. Visit https://durrantlab.com/blendmol/ to download the BlendMol ZIP file.
  2. Within Blender, click on the Edit > Preferences... menu item to open the Blender Preferences window.
  3. Click the Add-ons button at the top of that window to open the add-ons panel.
  4. Specify the location of the downloaded ZIP file by clicking on the Install... button at the bottom of the window.
  5. Once installed, click the Import-Export: BlendMol - PDB/VMD checkbox to activate the plugin.
  6. To keep the plugin active after Blender restarts, you may need to check the Save Preferences option via the hamburger menu at the bottom of the window.
  7. Critical plugin preferences can be set from the Add-ons panel by clicking the expanding carat. See the BlendMol manuscript for full details.

Detailed Installation Instructions

(Note that some of the details in the pictures below are outdated, but they still illustrate the basic steps.)

Download the BlendMol plugin.

Click Edit -> Preferences... to install the plugin.

Edit -> Preferences...

Click the Install... button.

Install...

Select the BlendMol ZIP file and click the Install... button.

Install...

Tick the checkbox (yellow) to activate the plugin. Then click the down caret button (red) to show the plugin options. Specify the location of the VMD executable using the appropriate button (green).

VMD Executables

If you would like BlendMol to auto load when you restart Blender, use the Save Preferences option.

Save Preferences

BlendMol Usage

(Note that some of the details in the pictures below are outdated, but they still illustrate the basic steps.)

Basic Usage

Basic Usage Video Tutorial

Click File -> Import -> PDB/VMD (.pdb, .vmd, .tcl).

File -> Import -> PDB/VMD (.pdb, .vmd, .tcl)

To load a PDB file, select the filename. Additional options (not shown) are given in a panel to the left. When ready, press the Import PDB/VMD/TCL button.

Import PDB/VMD/TCL

VMD state files can be similarly loaded.

Import PDB/VMD/TCL

Import PDB/VMD/TCL

You can also type a PDB ID into the filename field (boxed in red). BlendMol will download the PDB model directly from the Protein Data Bank.

Import PDB/VMD/TCL

Advanced Usage

Video S2: Neuraminidase

Video S2: Neuraminidase

Creating Video S2 required the use of many advanced Blender features that are unrelated to BlendMol's core functionality. A detailed tutorial is beyond the scope of this document, but interested users may benefit from the Blender Guru channel on YouTube, which provides many useful tutorials.

Video S3: BlendMol/Pyrite

Coupling BlendMol and Pyrite, another Durrant-lab plugin, simplifies the Blender-based visualization of molecular dynamics simulations.

Video S3: Pyrite Demo

Video S4: BlendMol/Pyrite Tutorial

Example Files

Example files can be found in ./examples/.

  • ./examples/vmd-files/ includes a PDB and VMD state file.
  • ./examples/web-files/baked-lighting-shadows/ demonstrates browser-based molecular visualization with advanced lighting and shadows.
  • ./examples/web-files/virtual-reality/ demonstrates browser-based virtual-reality molecular visualization.

About

BlendMol is a Blender plugin that can easily import VMD 'Visualization State' files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with a popular analysis program (VMD).

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