Spin, Bounce, Oscillate

This is how you make your molecule twirl, bounce or oscillate.


1 Open DejaVu.


2 Select Spin Settings.








3 Click Spin button to engage spinning.
4 Adjust using the Vector axes arrows.

Get a physical Model! Molecules in your Hand! Easier than PMV!!!

All you need is a PDB and an idea and we'll build an actual three-dimensional physical structure you can hold in your hand and pass from person to person. Actually we can use almost any file format to create your molecular model. Also, you may build your own model in PMV or pymol and send the session file our way. The cost of these models is determined by the volume of the model, the amount of Superglue used to hold it together, and the time it took to make. That is, $5/cubic inch, $10/ounce of superglue, and $25/ hour. Contact Jon Huntoon by phone (858) 784-2751 or by email huntoon@scripps.edu. Everything we make is custom. A normal model will take somewhere between 1 and 10 hours of modeling time, 1 to 50 cubic inches of material and 0.5 to 5 ounces of superglue, putting the price range at $50 to $500 most of the time. Please note there will be a 89.5% overhead fee for all models made for researchers outside of The Scripps Research Institute.

Build A Virus

Don't try to load that entire biological subunit, a whole virus file could contain a million atoms. You're going to crash your computer or at best move very slowly.

--This is for viruses with icosahedral symmetry similar to poliovirus and rhinovirus. For other icosahedral symmetries, some modifications may need to be applied.--

So here's the best thing to do:

1. Load your desired molecule. I am using the great 2plv, or poliovirus protomer. Poliovirus is a pretty simple structure, as you will see.

2. Open Vision, by clicking the button left of the sunglasses.

3. Load the SymServer Library from Libraries--> Load Libraries--> SymLib

4. From the PMV tab drag down your molecule's node and the 'set instances' node onto the blank canvas.

5. From the 'SymServer' tab, drag down the 'Icosahedral 1' node onto the canvas.

your map should look like this now:

6. DoubleClick the 'Icosahdral 1' node. Connect the 'input Ports' node to the '5-fold' node (blue box to blue box).

7. Connect your molecule's node to the 'Set Instances' node (purple oval to purple oval) and connect the 'Icosahedral 1' node to 'Set Instances' node as well ( blue box to blue box)

You should be golden now! You can make surfaces and color or anything you want, and the great thing about it is that your really only doing this to molecule instead of 60! This way, hardly any memory is used up!

-Jon Huntoon

Read an STL file

Here's how to read a Stereo-Lithographic file (.STL). STL files are a simple list of XYZ coordinates of vertices. They are geometry. If, for whatever reason, you want to import some shape, like a torus, or even and molecular surface you can! First you need that .stl.To save a .stl file in PMV, simply goto File--> Write--> Write STL. Or if you want some foreign shape use your 3D modelling program like Google SketchUp or Maya to save an stl.

1. Open Vision.

This button:

2. In Vision, load the Visualization Libarary, 'vizlib', under Libraries-->Load Library-->vizlib. 

3. a Drag down the 'Read STL ASCII' node from the 'deprecated' list in to the blank canvas area.

    b Drag down the 'PMV Viewer' node from the PMV tab under the PMV list.

    c Double-click the 'Read STL ASCII' node and load your STL file.

    d Connect the two nodes by dragging a line from the bottom blue circle of 'Read STL ASCII'            to the top red box of 'PMV Viewer'.

Now, that torus or whatever should be present in the viewer.

BONUS #1: This geometry will be listed in the DejaVu GUI. 

BONUS #2: You can connect the torus to a pdb by binding the geometry to the molecule under '3D Graphics'--> 'Bind Geometry to Molecule'. Then you can color that torus by atom type proximity just as you would any other surface. 

-Jon Huntoon

Select the HET Atoms

Want to select small molecules and co-factors? The atoms that aren't part of standard residues, like drugs, cholesterols, Zn atoms, and all else? 

Things like this:

HETATM 2185  O6  MAN A1310      78.725  55.327  98.231  1.00 81.20           O  

HETATM 2186 ZN    ZN A1311      62.745  46.321 102.600  1.00 38.48          ZN  

HETATM 2187 CL    CL A1312      59.817  29.875  99.087  1.00 40.97          CL  

HETATM 2188 CL    CL A1313      41.111  19.647  77.717  1.00 38.39          CL  

HETATM 2189  O   HOH A2001      59.085  17.513  98.258  1.00 65.67           O  

from your PDB file...

Here's how:

1 To select the HET atoms, goto Select--> Select from String. 

2 Under the 'atom' field, type: lambda x: x.hetatm == 1

3 Click 'Add' and your HET atoms will be selected. 

-Jon Huntoon

Opacity

Sometimes you need to see what's below the surface. Here is one way: lower the opacity of the surface... & here is how:

1. Start with a Molecular surface, and a ribbon. Calculate these under Compute--> MSMS, and Compute--> Secondary Structure-->Ribbon. Color the Ribbon by Secondary Structure.

2. The surface is now hiding the ribbon. To see both the ribbon AND the surface, Open the DejVu GUI.

3. Select the MSMS-MOL surface.

4. Under 'Material' deselect the 'inherit' property and then click the 'Front' box.

5. At the bottom of this Material Editor, there is a slider that controls opacity. Lower the opacity to about 50%.

6. Now you can see both your ribbon and your surface.

-Jon Huntoon

Electron Density Map

Here is how you can read and display an electron density map. These are important  to look at if you are to be critical of a particular PDB structure. 

1a Load PDB

1b Download the corresponding CCP4 file from PDB.

 

2a Create a Vision Network. 

 (middle button, boxes & lines, not the sunglasses button)

2b Load the Vis and Vol Libraries from Libraries--> Load Libraries....

 

2c Drag the following 'nodes' on to the blank 'canvas':

- 'Read Any Map' (Load CCP4 here) -from Vol Library (grey)

- 'Sample' (use a level 3 or two) - from Vol Library

- 'UT iso-contour' From Vol Library

- 'Ind Polygons' -from Vis Library (yellow)

- 'PMV Viewer' - from PMV Library (purple-ish/blue?... hmm. Periwinkle!)

(it helps to use the search box  to find these nodes)

Connect these nodes by dragging lines from the output ports (bottom square things) to the input ports(top square things) (colors should correspond [mostly]):

3 Double-click the UT iso-contour 'node' to see the isocontour graphs. Looks like this:

4 Drag the black vertical line to Pick an iso-value that suits your purposes. It will be hairy, so you may want to...

5 Open DejaVu  (it's the left-erly button with a cube, sphere and pyramid) to adjust opacity and or clipping  of the IndPolygons geometry  you just created!

And you can end up with something like this or (probably) better. Explore around. Have fun. Get good.

--

Jon Huntoon