BlendMol
Table of Contents
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:
- Visit https://durrantlab.com/blendmol/ to download the BlendMol ZIP file.
- Within Blender, click on the
Edit > Preferences...menu item to open theBlender Preferenceswindow. - Click the
Add-onsbutton at the top of that window to open the add-ons panel. - Specify the location of the downloaded ZIP file by clicking on the
Install...button at the bottom of the window. - Once installed, click the
Import-Export: BlendMol - PDB/VMDcheckbox to activate the plugin. - To keep the plugin active after Blender restarts, you may need to check
the
Save Preferencesoption via the hamburger menu at the bottom of the window. - 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(Note that some of the details in the pictures below are outdated, but they still illustrate the basic steps.)
Click Edit -> Preferences... to install the plugin.
Click the Install... button.
Select the BlendMol ZIP file and click the Install... button.
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).
If you would like BlendMol to auto load when you restart Blender, use the
Save Preferences option.
BlendMol Usage
(Note that some of the details in the pictures below are outdated, but they still illustrate the basic steps.)
Basic Usage
Click 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.
VMD state files can be similarly loaded.
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.
Advanced Usage
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 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.