May 13, 2009

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

May 7, 2009

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

May 1, 2009

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
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