Kill the shine.

Do you ever get annoyed by how shiny molecules are? Every picture of a molecule I see shows a shiny shiny molecule, like it was made of alien-space-age-nasa-plastic. Here I show you how to kill that shine, making a dull earthlier look.

Easy to do: decrease specularity value to 0.08.

1. Open Deja vu. Select the 'Light' tab. Select 'Light Colors' box.

2. Set the drop down menu to "light 1- specular"

3. Adjust the Value from 80 (default) to 10 or below.

There's a lot of cool effects to be achieved by adjusting the values and colors of the various lights in the 'Light Colors' menu. Poke around to get a unique look.

Bonus: when you have a look you want to save, Bookmark it! In Deja vu, select 'Bookmarks' tab and click 'Save Representation'.

Calculate Volume

Quick: what is the volume of this molecular suface?

Here I present a simple method for calculating the volume of a geometric object in PMV.
1. Open Vision.
2. Load the Visualization Library.

3. Drag down the 'PolyhedronVolumeArea' node from the mapper menu and the 'Choose Geom' node from the filter menu in the Visualization library. Drag down the 'PMV Viewer' node in the PMV library. Drag down the 'PopUpMsg' from the Standard Library.

4. Arrange them: PMV Viewer to Choose Geom to PolyVolArea to PopUpMSG. See picture below:

Be sure to choose the geometry you'd like to calculate the volume for.
Here, I have chosen the molecular surface.

5. The volume will appear in the Python IDLE Shell.

Note: units are in Angstroms.

Measure Distance in PMV

Antibody molecule 1igt, with a wingspan of 152.411 Angstroms, or 15.2 nanometers.

1. Under 'Picking Commands', select 'measureDistanceGC'.

The 'Picking Commands' icon is a pointing hand in blue.

2. Select the two atoms you wish to measure the distance between.

Note: Units are Angstoms.

Ambient Occlusion in PMV

Antibody 1igt with Ambient Occlusion from PMV by Jon Huntoon

From wikipedia: "Ambient occlusion is a shading method used in 3D computer graphics which helps add realism to local reflection models by taking into account attenuation of light due to occlusion. Ambient occlusion attempts to approximate the way light radiates in real life, especially off what are normally considered non-reflective surfaces.
Unlike local methods like Phong shading, ambient occlusion is a global method, meaning the illumination at each point is a function of other geometry in the scene. However, it is a very crude approximation to full global illumination. The soft appearance achieved by ambient occlusion alone is similar to the way an object appears on an overcast day."

To achieve this sophisticated look is mostly unattainable in other viewing software. But PMV makes it painless. Here's how:

1. Open Deja Vu
2. Select Ambient Occlusion

3. Select the geometries you'd like to have ambient occlusion applied to and then click 'Add'.

4. Select cavity darkness and overall brightness (I left these settings default).
5. Click Compute.

That's all. Sit back and watch the computations chug away. My rendering took about 2 minutes on a new iMac. The other cool thing about this is that once the shadows are calculated, they remain. You don't need to recalculate every time the camera moves like you would in other 3D viewers. Have fun!

Here's what a secondary structure looks like with ambient occlusion turned on.

Ambient occlusion on secondary structure.
Note: the stick-and-balls didn't get rendered.

BONUS: In Deja Vu, select 'Scene Antialiasing' and increase the value to at least 8 for cleaner edges.

-Jon Huntoon