BradyAJohnston · BradyAJohnston · Jul 22, 2024 · Aug 2, 2024
diff --git a/docs/_quarto.yml b/docs/_quarto.yml
@@ -20,6 +20,7 @@ website:
 
       - installation.md
       - example_listings.qmd
+      - quick_reference.qmd
       - section: Tutorials
         contents: tutorials/*
       - section: Nodes

diff --git a/docs/images/CleanShot 2024-07-20 at [email protected] b/docs/images/CleanShot 2024-07-20 at [email protected]
diff --git a/docs/images/CleanShot 2024-07-20 at [email protected] b/docs/images/CleanShot 2024-07-20 at [email protected]
diff --git a/docs/images/CleanShot 2024-07-20 at [email protected] b/docs/images/CleanShot 2024-07-20 at [email protected]
diff --git a/docs/images/CleanShot 2024-07-20 at [email protected] b/docs/images/CleanShot 2024-07-20 at [email protected]
diff --git a/docs/images/swap_node_select_color.mp4 b/docs/images/swap_node_select_color.mp4
diff --git a/docs/images/swap_style_node.mp4 b/docs/images/swap_style_node.mp4
diff --git a/docs/quick_reference.qmd b/docs/quick_reference.qmd
@@ -0,0 +1,91 @@
+---
+title: "Quick Reference"
+format: html
+---
+
+## Swap Nodes
+
+### Swap Style Nodes
+
+You can quickly swap one style node for another, by first selecting then right clicking and using the `Swap Node` menu to change it for another style node.
+Connections to and from the node will be maintained.
+
+![](images/swap_style_node.mp4)
+
+### Swap Color and Select Nodes
+
+You can also swap the select and color nodes for other nodes from those categories.
+
+![](images/swap_node_select_color.mp4)
+
+## Transforming Objects
+
+### Keyboard Shortcuts
+
+-   Grab <kbd>G</kbd> : Grab and transform / move the currently selected object.
+-   Scale <kbd>S</kbd>: Scale the current object
+-   Rotate <kbd>R</kbd>: Rotate the selected object
+
+Lock the transforms to any of the axes by using the <kbd>X</kbd>, <kbd>Y</kbd>, <kbd>Z</kbd> keys after starting the transform.
+Lock the transform to be perpendicular to those axes by using <kbd>Shift</kbd> + *axis key*.
+
+### Origin Point
+
+All of the points in an object are relative to an origin point (the small orange dot that is visible when the object is selected).
+When rotating an object, it will be rotated around its origin point.
+You can cahcnge this origin by through the right click context menu and using the `Set Origin` submenu.
+
+### Clear Transforms
+
+To reset the rotation, translation or scale back to the original state, use the <kbd>Alt</kbd> + (<kbd>G</kbd> / <kbd>R</kbd> / <kbd>S</kbd>) to clear the transform for that transformation.
+
+### Apply Transforms
+
+<kbd>Ctrl</kbd> + <kbd>A</kbd> All of the objects in Blender are in reference to the word origin.
+Applying their transformations makes the current location, rotation and scale be the starting location, rotation and scale.
+Can help with fixing some rotation and offset issues.
+
+## Materials
+
+Materials for regular objects are set through the `Material` tab of the object.
+When using `Geometry Nodes` you must manually set the materials with a `Set Material` node.
+The Molecular Nodes `Style` nodes all set the material of their outputs.
+
+## Render Settings
+
+### Transparent Background
+
+Check the `Transparent` option under `Render Settings` -\> `Film` -\> `Transparent`.
+
+![](images/CleanShot%202024-07-20%20at%[email protected])
+
+### Output Resolution
+
+Change the output resolution of under `Output Properties` .
+This output resolution also changes the aspect ratio of the camera.
+For a portrait camera output - it is best to change the output resolution and not rotate the camera.
+
+![](images/CleanShot%202024-07-20%20at%[email protected])
+
+### Render Engine
+
+Changing the render engine is done under the `Render Properties` tab (the icon is the back of DSLR camera).
+When using `Cycles` render engine, if you computer supports it, you should likely enable `GPU Compute` to use your GPU for rendering which will likely be faster.
+
+### Render Samples
+
+The number of will determine how long Blender will spend rendering the image.
+The higher the samples, the longer it will spend calculating the final image and the less noisy the image will be.
+The more complex the lighting and materials are in your scene, the higher the samples you will need to get a less noisy result.
+It is worth experimenting with the number of samples you need when rendering an animation.
+If you can get away with lower numbers (\~256) it will save you a lot of render time.
+
+The `Denoise` option is for using AI denoising after rendering, so you can get away with lower samples for a similar result.
+If possible, I recommend changing the to use GPU.
+
+![](images/CleanShot%202024-07-20%20at%[email protected])
+
+
+### Backgrounds
+
+### Depth of Field
diff --git a/docs/tutorials/01_importing.qmd b/docs/tutorials/01_importing.qmd
@@ -7,6 +7,8 @@ Molecules, simulations and other file formats can all be imported via the `Molec
 
 ![The panel location.](images/panel-location.png)
 
+You can download protein structures directly from the PDB using their corrseponding codes.
+
 You can download a structure directly from the PDB, just from the accession code. Molecular Nodes will download the file as a `.bcif` file and cache it locally on your computer, then open the file in to Blender. This is the quickest way to import structures that are already available via the wwPDB. Currently this downloads via the RCSB.
 
 To download directly from the PDB, you can use the <kbd>PDB</kbd> tab.
@@ -40,6 +42,7 @@ While the molecule is imported, we are in 3D view by default. We can change to a
 ![Changing to rendered views in different rendering engines.](https://imgur.com/oF05D7S.mp4)
 
 ## Changing Styles
+![](images/)
 
 The protein is now imported in the scene. To change the way the protein is displayed, we have to use the `Geometry Nodes` editor. This is where we change the nodes that are use to process the underlying atomic data, resulting in the final 3D object we can see in front of us.