Commit 122646bb authored by Jacob Durrant's avatar Jacob Durrant

Updated tutorial for latest version of Pyrite and Blender.

parent 0c3ad597
Pipeline #275 failed with stages
Pyrite 1.1.0
============
# Pyrite 1.1.0
## 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
......@@ -9,8 +10,7 @@ the terms of the GNU General Public License Version 3. [Click here](https://durr
If you use Pyrite, please [cite our paper](https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.25155).
The Latest Version
==================
## The Latest Version
To view the source code of the latest version, visit
[http://git.durrantlab.com/jdurrant/pyrite](http://git.durrantlab.com/jdurrant/pyrite).
......@@ -18,43 +18,37 @@ The same code is mirrored on GitHub.
Visit [http://durrantlab.com/pyrite/](http://durrantlab.com/pyrite/) to:
* read the documenation
* read the documentation
* suggest an improvement
* point out a bug
* ask a question about usage
Installation
============
## Installation
Pyrite installation within Blender is the same as with any Blender plugin:
1. Visit [http://durrantlab.com/pyrite/](http://durrantlab.com/pyrite/) to
download the Pyrite ZIP file.
2. Within Blender, click on the ```File > User Preferences...``` menu item to
open the ```Blender User Preferences``` window.
3. Click the ```Add-ons``` button at the top of that window to open the
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 Add-on from File...``` button at the bottom of the window.
5. Once installed, click the ```3D View: Pyrite``` checkbox to activate the
plugin.
6. To keep the plugin active after Blender restarts, click the ```Save User
Settings``` button at the bottom of the window.
```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
====================
## Authors and Contacts
Pyrite was produced by Jacob Durrant
([durrantj@pitt.edu](mailto:durrantj@pitt.edu)) with the assistance of Nivi
Rajendiran.
Tutorial
========
## Tutorial
1. Create a Protein or Nucleic-Acid Mesh
----------------------------------------
### 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
......@@ -63,7 +57,7 @@ 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:
```
```tcl
set m {
{{1.0 0.0 0.0 0.0}
{0.0 1.0 0.0 0.0}
......@@ -91,7 +85,7 @@ for {set i 0} {$i < [molinfo num]} {incr i} {
In PyMOL, the same can be accomplished with this Python script, which moves
and rotates the camera to the appropriate location:
```
```python
cmd.set_view([ 1.0, 0.0, 0.0,
0.0, 1.0, 0.0,
0.0, 0.0, 1.0,
......@@ -104,8 +98,7 @@ 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
---------------------------
### 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
......@@ -117,11 +110,10 @@ 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
Tool Shelf Panel will automatically set these vectors. You can also set the
Sidebar Panel will automatically set these vectors. You can also set the
values in Blender’s Object Properties Panel.
3. Specify the Trajectory File
------------------------------
### 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
......@@ -130,8 +122,7 @@ saved in other formats (e.g., the binary DCD format) can be converted to PDB
using [VMD](http://www.ks.uiuc.edu/Research/vmd/) or
[catdcd](http://www.ks.uiuc.edu/Development/MDTools/catdcd/).
4. Set the Trajectory-Simplification Options
--------------------------------------------
### 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
......@@ -139,8 +130,7 @@ 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
-----------------------------
### 5. Create High-Detail Regions
You may wish to more accurately represent the MD-captured motions of some
regions (e.g., active sites):
......@@ -160,8 +150,7 @@ regions (e.g., active sites):
You can add several spheres to the scene if multiple distinct regions require
higher spatial resolution.
6. Load the Trajectory
----------------------
### 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
......
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