Pyrite 1.1.1

Description

"Pyrite" is a program for importing a molecular dynamics trajectory into Blender, to take advantage of Blender's advanced rendering features. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. Click here for a video tutorial.

If you use Pyrite, please cite our paper.

The Latest Version

To view the source code of the latest version, visit http://git.durrantlab.com/jdurrant/pyrite. The same code is mirrored on GitHub.

Visit http://durrantlab.com/pyrite/ to:

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

Installation

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

1. Visit http://durrantlab.com/pyrite/ to download the Pyrite 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 left 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: Pyrite checkbox to activate the plugin.
6. To keep the plugin active after Blender restarts, you may need to use the Save Preferences option.

Authors and Contacts

Pyrite was produced by Jacob Durrant (durrantj@pitt.edu) with the assistance of Nivi Rajendiran.

Tutorial

1. Create a Protein or Nucleic-Acid Mesh

Free programs such as VMD, PyMOL, and Chimera export molecular representations in Blender-compatible formats (e.g., OBJ, WRL, X3D, etc). Exported mesh files use camera coordinates rather than the world coordinates of the original model. Before exporting, all transformation matrices must be set to identity. In VMD, this simple TCL script, adapted from code provided by John Stone (VMD’s primary developer), sets the coordinate system:

set m {
  {{1.0 0.0 0.0 0.0}
   {0.0 1.0 0.0 0.0}
   {0.0 0.0 1.0 0.0}
   {0.0 0.0 0.0 1.0}}
  {{1.0 0.0 0.0 0.0}
   {0.0 1.0 0.0 0.0}
   {0.0 0.0 1.0 0.0}
   {0.0 0.0 0.0 1.0}}
  {{1.0 0.0 0.0 0.0}
   {0.0 1.0 0.0 0.0}
   {0.0 0.0 1.0 0.0}
   {0.0 0.0 0.0 1.0}}
  {{1.0 0.0 0.0 0.0}
   {0.0 1.0 0.0 0.0}
   {0.0 0.0 1.0 0.0}
   {0.0 0.0 0.0 1.0}}
}

for {set i 0} {$i < [molinfo num]} {incr i} {
  molinfo ${i} set {center_matrix rotate_matrix scale_matrix global_matrix} $m
}

In PyMOL, the same can be accomplished with this Python script, which moves and rotates the camera to the appropriate location:

cmd.set_view([ 1.0,   0.0,   0.0,
               0.0,   1.0,   0.0,
               0.0,   0.0,   1.0,
               0.0,   0.0,   0.0,
               0.0,   0.0,   0.0,
              40.0, 100.0, -20.0])

After setting up the scene in your program of choice (e.g., using ribbon or surface representation for the proteins), export the first frame as an OBJ file.

2. Import Mesh into Blender

Import your Wavefront OBJ file using Blender's menu: File > Import > Wavefront (.obj). After importing the mesh, prepare it for animation. For example, using Blender's "Remove Doubles" command is often critical. Available in Edit Mode, this command merges duplicate vertices into one to ensure that all mesh faces are connected.

Blender itself sometimes imports meshes using the incorrect coordinate system. Setting the object position and rotation vectors to (0.0, 0.0, 0.0), and the scaling vector to (1.0, 1.0, 1.0), ensures that the imported object and trajectory use the same system. Pressing the "Auto-Fix" button in Pyrite's Sidebar Panel will automatically set these vectors. You can also set the values in Blender’s Object Properties Panel.

3. Specify the Trajectory File

If an object has the appropriate transformation vectors, the Pyrite tab presents options for simulation import. Use the first option to specify the location of the MD trajectory file, in multi-frame PDB format. Trajectories saved in other formats (e.g., the binary DCD format) can be converted to PDB using VMD or catdcd.

4. Set the Trajectory-Simplification Options

Loading the position of every atom across the entire MD trajectory is often too memory and CPU intensive. Instead, Pyrite coarse grains the simulation across time and space by discarding some frames and atoms. Select the temporal and spatial resolution by indicating how often to keep a frame or atom (e.g., only every nth frame and every mth atom).

5. Create High-Detail Regions

You may wish to more accurately represent the MD-captured motions of some regions (e.g., active sites):

1. Add a sphere to Blender's viewport by positioning the 3D cursor and clicking the "Create Region" button in the "High-Detail Regions" subpanel.
2. Adjust the position and scaling until the sphere encompasses the region of interest.
3. Use the Pyrite panel to specify how often to keep atoms within the sphere. By selecting a lower skip/stride value, fewer atoms within the sphere-defined region are discarded. The captured MD motions within this region will have higher spatial resolution.
4. After positioning and scaling the sphere, press the "Back to Mesh" button to save. Alternatively, the "Delete Region" button will remove the current sphere.

You can add several spheres to the scene if multiple distinct regions require higher spatial resolution.

6. Load the Trajectory

After saving the high-detail regions, press the "Load Trajectory" button to import trajectory data. Empty objects populate the viewport at the locations of the retained atoms.