Basics of VMD

In this unit you will build a nice image of ubiquitin while becoming accustomed to basic VMD commands. In addition, you will learn how to look for interesting structural properties of proteins using VMD.

Loading a Molecule

Our first step is to load our molecule. A pdb file, 1UBQ.pdb, that contains the atom coordinates of ubiquitin is provided with the tutorial.

1

Choose the File $\rightarrow$ New Molecule... menu item Fig. 2(a) in the VMD Main window. Another window, the Molecule File Browser (b), will appear in your screen.

2

Use the Browse... (c) button to find the file 1UBQ.pdb in vmd-tutorial-files. Note that when you select the file, you will be back in the Molecule File Browser window. In order to actually load the file you have to press Load (d). Do not forget to do this!

Figure 2: Loading a Molecule.

Now, ubiquitin is shown in your screen in the OpenGL Display window. You may close the Molecule File Browser window at any time.

Displaying the Protein

In order to see the 3D structure of our protein we will use the mouse in multiple modes.

1

In the OpenGL Display, press the first (left) mouse button down and move the mouse. Explore what happens. This is the rotation mode of the mouse and allows you to rotate the molecule around an axis parallel to the screen Fig. 3(a).

Figure 3: Rotation modes.

2

If you press the second (right) button and repeat the previous step, the rotation will be done around an axis perpendicular to your screen (b) (For Mac users, the second button is equivalent to hitting the command key while pressing the mouse button).

3

In the VMD Main window, look at the Mouse menu (Fig. 4). Here, you will be able to switch the mouse mode from Rotation to Translation or Scale modes.

4

The Translation mode will allow you to move the molecule around the screen while holding the first (left) button down.

Figure 4: Mouse modes.

5

The Scale mode will allow you to zoom in or out by moving the mouse horizontally while holding the first (left) button down.

It should be noted that the previous actions performed with the mouse do not change the actual coordinates of the molecule atoms.

Another useful option is the Mouse $\rightarrow$ Center menu item. It allows you to specify the point around which rotations are done.

6

Select the Center menu item and pick one atom at one of the ends of the protein; The cursor should display a cross.

7

Now, press r, rotate the molecule with the mouse and see how your molecule moves around the point you have selected.

Exploring Different Drawing Styles

VMD can display your molecule using a wide variety of drawing styles. Here, we will explore those that can help you to identify different structures in the protein.

1

Choose the Graphics $\rightarrow$ Representations... menu item. A window called Graphical Representations will appear and you will see highlighted in yellow Fig. 5(a) the current graphical representation used to display your molecule.

2

In the Draw Style tab (b) we can change the style (d) and color (c) of the representation. In this section we will focus in the drawing style (the default is Lines).

3

Each Drawing Method has its own parameters. For instance, change the Thickness of the lines by using the controls on the right bottom part (e) of the Graphical Representations window.

4

Now, choose VDW(van der Waals) from Drawing Method. Each atom is now represented by a sphere. In this way you can see more easily the volumetric distribution of the protein.

Figure 5: Graphical Representations window.

5

To see the arrangements of atoms in the interior of the protein, use the new controls on the right bottom part of the window (e) to change the Sphere Scale to 0.5 and the Sphere Resolution to 13. Be aware that the higher the resolution, the slower the display of your molecule will be.

6

Note in Coloring Method $\rightarrow$ Name, each atom has its own color, i.e: O is red, N is blue, C is cyan and S is yellow.

7

Press the Default button. This allows you to return to the default properties of the drawing method.

The previous representations allow you to see the micromolecular details of your protein. However, more general structural properties can be seen by using more abstract drawing methods.

8

Choose the Tube style under Drawing Method and observe the backbone of your protein. Set the Radius at 0.8.

9

By looking at your protein in the tube mode, can you distinguish how many helices, $\beta$ sheets and coils are present in the protein?

The last drawing method we will explore is NewCartoon. It gives a simplified representation of a protein based in its secondary structure. Helices are drawn as coiled ribbons, $\beta$ sheets as solid arrows and all other structures as a tube. This is probably the most popular drawing method to view the overall architecture of a protein.

10

Choose Drawing Method $\rightarrow$ NewCartoon.

11

Identify now how many helices, betasheets and coils are present in the protein.

Figure 6: Licorice, Tube and NewCartoon representations of Ubiquitin

Exploring Different Coloring Methods

1

Now, let's modify the colors of our representation. Choose Coloring Method $\rightarrow$ ResType Fig. 5(c). This allows you to distinguish non-polar residues (white), basic residues (blue), acidic residues (red) and polar residues (green).

2

Select Coloring Method $\rightarrow$ Structure (c) and confirm that the NewCartoon representation displays colors consistent with secondary structure.

Exploring Different Selections

Let's look at different independent (and interesting) parts of our molecule.

1

In the Selected Atoms text entry Fig. 5(f) of the Graphical Representations window delete the word all, type helix and press the Apply button or hit the Enter/Return key on your keyboard. (Do this every time you type something.) VMD will show just the helices present in our molecule.

2

In the Graphical Representations window choose the Selections tab Fig. 7(a). In section Singlewords (b) you will find a list of possible selections you can type. For instance, try to display $\beta$ sheets instead of helices by typing the appropriate word in the Selected Atoms text entry.

Combinations of boolean operators can also be used when writing a selection.

3

In order to see the molecule without helices and $\beta$ sheets, type the following in Selected Atoms: (not helix)and(not betasheet)

4

In the section Keyword (c) of the Selections tab (a) you can see properties that can be used to select parts of a protein with their possible values. Look at possible values of the Keyword resname (d). Display all the Lysines and Glycines presents in the protein by typing (resname LYS)or(resname GLY). Lysines play a fundamental role in the configuration of polyubiquitin chains.

5

Now, change the current representation's Drawing Method to CPK style and the Coloring Method to ResID in the Draw Style tab. In the screen you will be able to see the different Lysines and Glycines. How many of each one can you see?

6

In the Selected Atoms text entry type water. Choose Coloring Method $\rightarrow$ Name. You should see the 58 water molecules (in fact only the oxygens) present in our system.

7

In order to see which water molecules are closer to the protein you can use the command within. Type water and within 3 of protein. This selects all the water molecules that are within a distance of 3 angstroms of the protein.

Figure 7: Graphical Representations window and the Selections tab.

8

Finally, try typing the following selections in Selected Atoms:

Selection	Action
protein	Shows the Protein
resid 1	The first residues
(resid 1 76) and (not water)	The first and last residues
(resid 23 to 34) and (protein)	The $\alpha$ helix

All the previous options provide you with a powerful tool to explore different parts of your protein or molecule.

Multiple Representations

The button Create Rep Fig. 8(a) in the Graphical Representations window allows you to create multiple representations. Therefore, you can have a mixture of different selections with different styles and colors, all displayed at the same time.

1

For the current representation, set the Drawing Method to NewCartoon and the Coloring Method to Structure.

2

In Selected Atoms type protein.

3

Press the Create Rep button (a). Now, using the menu items of the Draw Style tab and the Selected Atoms text entry, modify the new representation in order to get VDW as the Drawing Method, ResType as the Coloring Method, and resname LYS typed in as the current selection.

Figure 8: Multiple Representations of Ubiquitin.

4

Repeating the previous procedure, create the following two new representations:

Drawing Style	Coloring Method	Selection
CPK	Name	water
VDW	ColorID 1	resid 1 76 and name CA

5

Create a final representation by pressing again the Create Rep button. Select Drawing Method $\rightarrow$ Surf, the Coloring Method $\rightarrow$ Molecule and type protein in the Selected Atoms entry. For this last representation choose in the Material section (c) the Transparent menu item.

6

Note, that with the mouse, you can select the different representations you have created and modify each one independently. Also, you can switch each one on/off by double-clicking on it or delete each one by using the Delete Rep button (b). At the end of this section, the Graphical Representations window should look like Fig. 8.

Sequence Viewer Extension

When dealing with a protein for the first time, it is very useful to find and display different amino acids quickly. The sequence viewer extension allows you to pick and display one or more residues easily.

1

Choose the Extensions $\rightarrow$ Analysis $\rightarrow$ Sequence Viewer menu item. A window Fig. 9(a) with a list of the amino acids (e) and their properties (b)&(c) will appear in your screen.

2

With the mouse, click over different residues (e) in the list and see how they are highlighted. In addition, the highlighted residue will appear in your OpenGL Display window in yellow and bond drawing method, so you can visualize it easily. Use the right button of the mouse to unselect residues.

3

Using the Zoom controls (f) you can display the entire list of residues in the window. This is especially useful for larger proteins

4

Using the shift key while pressing the mouse button allows you to pick multiple residues at the same time. Look at residues 48, 63, 11 and 29 (e).

Figure 9: Sequence window.

5

Look at the Graphical Representations window, you should find a new representation with the residues you have selected using the Sequence Viewer Extension. As you already did before, you can modify, hide or delete this representation.

Information about residues is color-coded (d) in columns and obtained from STRIDE. The B-value column (b) shows the B-value field (temperature factor). The struct column shows secondary structure (d), where each letter means:

Table 1: Secondary Structure codes used by STRIDE.

T	Turn
E	Extended conformation ($\beta$ sheets)
B	Isolated bridge
H	Alpha helix
G	3-10 helix
I	Pi helix
C	Coil

Saving your Work

The image that you have created using VMD can be saved, along with all representations you have created, as a VMD state. This VMD state contains all the information needed to start a new VMD session from it, without losing what you have done.

1

In the VMD Main window, choose the File $\rightarrow$ Save State menu item. Write an appropriate name (e.g., myfirststate.vmd) and save it.

The File $\rightarrow$ Load State menu item will allow you to load a previously saved VMD state, just like the file you saved. Although the VMD state allows you to work with the image and explore the properties of our protein using VMD, you usually need pictures that can be used in articles or other kind of documents. VMD can render the image you created and generate an image file that can be used in other applications, as it is shown in the following steps.

2

Using all that you have learned until now, find an appropriate view of the protein by scaling, rotating and translating the molecule. Turn different representations on and off and improve the resolution and different properties of the selections you have made. If you want an image of high quality, put special attention to the resolution of each representation.

3

Be aware of the new representations you created with the Sequence Viewer Extension and hide or delete them if necessary.

4

Before rendering the image, change the background color by choosing the Graphics $\rightarrow$ Colors menu item. There, Choose the Display category, the Background name and the 8 white color. The background should be white now.

5

Choose the File $\rightarrow$ Render... menu item. A window called File Render Controls will appear in your screen.

6

You can render the image using different packages. Pick TachyonInternal in the Render using menu.

7

Write the name of the file where the image will be saved in the Filename text entry, i.e., picture.tga (default is plot.tga).

8

Press the Start Rendering button and the file with your image will be created. Note that this could take some time. You should end up with an image file named picture.tga (MacOS X or Unix) or picture.bmp (on Windows).

9

Close the application that opened the image file in order to continue using VMD.

Now you are done with the first unit of the tutorial. We hope you have learned the basic commands of VMD. Also, you have generated two files. The first one is a VMD state that allows you to restart a VMD session, and use or modify all that you did in this unit. The second file is an image file of your protein that can be used in other image-viewing applications.