Molecular Dynamics Group, University of Queensland
Molecular Dynamics Group, University of Groningen

MD

Tutorial

Visualization of the Structure



After having downloaded the file with the structural information on lysozyme, go to the terminal window and list the files in your subdirectory by typing 'ls'. It will show '1AKI.pdb' there.

Look at the contents of the file by entering the command 'more 1AKI.pdb'. Every line starts with a label. The first sections provide information on the techniques used and other annotations ('REMARK'). The actual structural data is found following the labels 'ATOM' and 'HETATOM'. Search the part with this data and try to understand the format. To get a brief introduction to the pdb (and other relevant) file types, follow this link.

Several packages are available for visualization, like RasMol and VMD. Focus will lie on VMD here, since it offers more options. VMD stands for 'Visual Molecular Dynamics'. To start it, type 'vmd' at the command prompt and press 'Enter'.

Three windows will appear when VMD is started:

To view the structure of the protein, select the option 'File' in the main menu. Then select 'New Molecule' and type 1AKI.pdb in filename section. Finally click on 'Load'.

The structure is now loaded and displayed rotating. Notice that VMD has converted the information contained in the pdb file to the structure shown. Also notice that the pdb file only contains coordinates for the atoms, but VMD also displays bonds.

To stop the structure from rotating simply click the left mouse button in the display window. The window still remains in rotation mode, and by clicking and dragging you can rotate the structure yourself (releasing the mouse button while dragging will give the structure a spin and it will keep rotating in the given direction).

VMD Basic Options



This section provides some explanation and simple exercises, to get acquainted with some of the basic options of VMD. This is based on the VMD workshop which can be found at http://www.ks.uiuc.edu/Research/vmd/workshop/main/main.html.

Scaling, rotating and translating



These are the three basic mouse modes in VMD. To switch to a certain mode press r(otate), s(cale) or t(ranslate) on the keyboard, while the mouse is in the display window. Try each mode and note how the cursor changes to indicate the current operation. For rotations, the left mouse button controls rotation about axes parallel to the screen while the right mouse button controls rotation about the axis perpendicular to the screen. In translation mode, the left mouse button controls translation parallel to the screen, while the middle button controls translation in and out of the screen. Finally, in scaling mode, both the left and middle buttons control global scaling when the mouse is moved left or right, but the middle button causes larger changes.
It is also possible to switch to a certain mode from the main menu. Select Mouse  and then click on  Translate Mode, Rotate Mode or Scale Mode.

Display styles



Multiple Renderings (display styles): Read this together with the next section related to atom selection as the two concepts are often used together. First activate the graphics form (select the option Graphics in the main menu) and go to Representations. All renderings for your molecule will be summarized in the blue browser list found on that form. To add a new rendering, click on the 'Create Rep' button on the bottom of this graphics menu. Notice that an extra line appears in the browser listing. In the text entry blank under the words 'Selected Atoms', type in an expression which describes the atoms that you would like to represent in a different style. Then using the drop down menu next to the words 'Drawing Method', choose a new representation for your selection. For example, choose 'Licorice'. You will notice that all atoms in the protein change in the GL Display. However the rest of the protein will appear unaltered, since you have not replaced the original rendering style, you have just added a new definition to it.

Atom selection



VMD has a powerful atom selection syntax from which one can describe groups of atoms in a variety of ways. You can see this syntax in the text entry box on the graphics menu. Rather then remembering the details of this syntax you can click on the Selections sections of the Graphical Representations menu. This gives you two browser windows listing properties from which you can identify groups of atoms: Singlewords browser show the syntax that can be use in the sections Selected Atom. Items in the 'Keyword' browser are also part of the selection syntax. If you click on one of these keywords, you will notice that available options for that keyword show up in the browser at the right. The best way to use these windows is as follows: First select 'Reset' at the bottom of the form. Then double click on the keywords you will use. This keyword now appears in the text entry (Selected Atom). Next, double click each 'Value' you would like to include as an option to this keyword. If you select 'Apply' button in the  menu, your request will be updated. For example, select 'Reset', double click 'Structure', and double click H. It now shows 'structure H' in the text entry box. Select 'Apply' and now only the alpha helices of lysozyme remain visible. Remember to select the 'Draw Style' menu to get back to controls for drawing and coloring methods.

To pick an atom: First select Mouse in the main menu and go to Label and select  Atoms. Then select Graphics and go to Labels. Open the labels menu. If you click on an atom in the GL  you will notice that a label for that atom pops up on the screen and a text appear on the Labels menu . At times these labels are useful, but too many will clutter the view. To delete them, use the Labels menu.

Drawing method



Change the drawing method: Click on 'Drawing Method' and select the option 'Tube'. Try some other options to see what changes they make in the display.
When a 'Drawing Method' is chosen,  some options  will  appear on an menu on the right. I.e. 'Drawing Method' is set on Lines, the thickness of the lines can be modified changing the menu at the bottom of the menu. Try with 2 or 3 instead of 1.  Try other options in the display form to test available VMD features.

Orthographic and perspective: To switch between orthographic and perspective viewing: Activate the option 'Display' in main and choose the appropriate setting.

To make an object transparent: Under 'Graphics' select 'Material' and then 'Transparent'.

Saving and restoring


Saving your work: You may want to save your work so that you can regenerate the picture later.
Select File in the main menu, then go to Save states . This will bring up a window where you can enter a file name in which to save your work. In the text console, type 'filename', where filename is the name of the file in which to save your work. To restore a figure, from the command line, start VMD with the options 'vmd -e filename', where filename is the name of the file that was saved (this currently works for Unix version of VMD only). Or, after starting VMD, select File in the main menu, then go to Load states and type 'filename'.

Using the above and Hen Egg White Lysozyme try to:


There are many other structural properties of this protein that you could visualize with this software, e.g. charge surfaces, angles, calculate distances, etc. See the users guide at: http://­www.ks.uiuc.edu/­Research/­vmd/­current/­ug/­ug.html, or the basic tutorials in the web page of vmd). VMD is free and available under UNIX, LINUX and Windows.

Home
Introduction
Lysozyme
Getting Started
Visualization
MD Theory
MD Practice
Analysis
Finally

©2005 T.A.Wassenaar