Arking:JCAOligoTutoria24
This tutorial was adapted from the "Basic Tutorial For DeepView" available at http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/. I've simplified it somewhat to illustrate the basic operation of the program. For the full glory of DeepView, I recommend following the complete tutorial available at the above URL.
Download DeepView
Go to http://spdbv.vital-it.ch/disclaim.html, accept the disclaimer, and then download the file. On a windows machine, it will come down as a zip file. You should unzip the file, and then double click on spdbv.exe to launch the program. (There is no "installer" for DeepView, and you can launch it from anywhere).
DeepView is often referred to by different names including spdbv, Swiss view, and Swiss-PdbViewer...it's all the same program, just different names.
Download a File
There are several ways to get structure files (.pdb files) for viewing in DeepView. DeepView can access pdb files from the Protein Data Bank directly, but I'll show you how to get to things via pubmed. For this tutorial, we want to work with Hen Egg-White Lysozyme in complex with the trisaccharide inhibitor tri-(N-acetylglucosamine). The ID code for the file we want is 1HEW.
Go to www.pubmed.gov, type "Hen Egg-White Lysozyme" into the search box, put the search pulldown menu on "Structure" and hit GO. This will pull up a lot of hits of different structures of Lysozyme. Each entry is a distinct crystal structure. Often the different hits are mutants of the original, different inhibitors bound to the protein, or maybe just another author's structure of the same protein. Unless you know specifically what ID file you want, you usually use keyword searches and browsing through the list to find what you are looking for. For this example, we know exactly what we want: 1HEW.pdb. So, type "1HEW" in the search box and hit GO. You should get this:
Click on the image, and that should take you to a screen that looks like this:
I've circled the link you should now follow to get to the Protein Data Bank where you can download the file. Click it.
I've circled the link to click to download the pdb file. Click it and save the file to your desktop. Now you can open it into DeepView. Double-clicking the desktop icon might do the job. If not, do "File > Open PDB File..." within DeepView to open the file. There might be some error messages that pop up. If you really want it not to give you these error messages, you can turn them off in the DeepView preferences. Just say ok to get rid of them for now. You should have something that looks like this:
If you don't have that rightmost window, the "Control Panel", you should open it up from the Window menu. Alright, now let's play with it!
Selecting and Displaying
You use the Control Panel to select, display, or hide parts of the model. Different parts of the model such as amino-acid residues or hetero groups like the three NAG residues in the lysozyme inhibitor are all called "groups" in DeepView. Selecting groups does not change the display. But most actions that you take on the model affect only the currently selected groups. The Control Panel lists all the groups in the model and allows you to select, hide, and display them. You may find this Panel imposing at first, but when you get the hang of it, you will be able to control the display and determine the targets of commands very quickly and precisely.
Click anywhere on the Control Panel window to make it active. First, simply scroll down to the bottom of the list to see how many amino-acid residues the protein contains, and to see how the hetero groups are named at the bottom of the list (hetero groups are always listed last). The tri-NAG inhibitor is listed as three residues of NAG, numbered 201 to 203.
Now click and drag, starting on the word GLY4 at the top of the window, dragging down to GLY16 and releasing the mouse button. All group names from GLY4 through GLY16 should turn red. Groups printed in red are now selected. The simplest way to select a small number of residues is to click their names and drag to select a range of them.
Now hit <Enter>. This will hide all groups except those selected. Now, let's center the view. There are different mouse modes that controls what happens to the display when you click or drag in the graphics window:
Click the button for "Scale and center visible groups". For now on, I'll just refer to this as "centering the view". Notice that after centering, the model rotates about the center of the groups on display. You are looking at residues 4 through 16 of the protein. Notice that a checkmark (on Windows, a checkmark looks like the letter v) has appeared in the "show" column next to the selected residues in the control panel, indicating that they are on display. There are checks also in the "side" column, which means that side chains are shown. A side chain is shown only if the rest of the residue is shown, so you only see the side chains of displayed residues in the graphics window.
Click the check in the side column next to MET12, to hide the side chain. Click the same space again to replace the check and display the MET12 sidechain. Try the same thing in the show, label (text labels), and surface (dotted van der Waals surface) columns, and look at the effects. Now remove the checks from the label and surface columns.
Again select and display residues 4-16 with side chains.
You can also turn on a whole column-worth of settings at once. To do this for just the selected groups, you click the header word at the top of a column in the Control Panel. Let's do this for "ribn". With residues 4-16 still selected, click on the word "ribn". You should get a little alpha helix showing up.
You can also turn on or off an entire column-worth of settings for the entire model with shift-clicks. To remove the labels, surface, and ribbon, hold down the shift key and click any checkmark in the label column (not the word label). Repeat for the surface and ribn columns. When you click on a checkmark while holding down shift, your action removes all checkmarks, and DeepView makes the corresponding changes in the display. You can also turn the whole column on by shift-clicking on an unchecked position in the column. So, you can toggle the view to be all-on or all-off by using shift-click for a particular column of settings.
Next, select and show residues 4-16 with their side chains, and add residues 17 through 22 as follows: click in the show column next to LEU17, drag down the column to GLY22, and release the mouse button. Arrows should appear in the show column next to residues 17 through 22, but these residue names should not turn red. If you drag too far, release the mouse button and then remove unwanted checkmarks by clicking them one at a time. Add checkmarks in the side column for residues 17-22 in the same way. Now residues 4 through 16 are selected and shown, while residues 17 through 22 are shown, but not selected.
<enter> (NOT return, but enter) (Note for Windows users: Instead of the enter key, use the + key of the numeric keypad)
Linux: use 'enter' on the numeric keypad, with Num Lock off..
Notice the result on both the Control Panel and the model. Press enter again. The enter key toggles the display (show) of selected groups on and off, without affecting other groups. Press enter several times, and be sure you understand what is happening. End with residues 4-22 displayed, but only residues 4-16 selected. Now press return. This shows all selected groups, and hides all unselected groups. Notice the difference between the return and enter keys: the return key adds selected groups, and removes unselected groups, while the enter key toggles between showing and hiding selected groups, without affecting unselected groups.
Again, display residues 4-22 (all with check in the show column, but with only residues 4-16 selected (red). Notice the + and - symbols above the Control Panel column headings. Try clicking them and see if you can figure out their functions. In short, these act as buttons to turn the column function (show, side, label, and so forth) on or off, but only for the selected groups.
Now let's consider how to make complex selections, without having to click individual entries.
For easily selecting a range of residues, click on a name to select the first residue, then hold down shift while clicking the last residue in the desired range. DeepView selects your first and last residue, and all those in between. Try it.
You can also select groups of residues that are not consecutive. With residues 4-16 selected and shown, hold down the control key (ctrl) and click TYR20 and LEU25. This adds residues 20 and 25 to the selection (shown in red). Press return to add them to the display. These residues are disconnected from the others. If you do not see them, Zoom/Center to center the displayed groups. Click the word side at the top of the Control Panel. This adds side chains to the newly selected groups. Note again that clicking headings in the Control Panel affects the selected residues only.
There are also two narrow columns to the left of the group column. The first column is blank when the current model contains only one protein chain, as does 1HEW.pdb (if the model contained more than one chain, the one-letter chain designations would appear in this column). Click anywhere in the first, blank column. You have selected the entire chain (in this case, the entire model). Press return and then help or = to see the entire model.
Linux: The use of the control key to add residues to current selection may not work in v 3.5.
The second column contains groups of the letters h or s. Groups labeled h comprise alpha helices, while groups labeled s comprise strands of beta sheet. Click on any h. You have selected the entire helix containing the residue you chose. Zoom and center the helix. Now find a different helix in the Control Panel list. Hold down ctrl and click any h in your chosen helix. You have added the second helix to the display (without selecting it). Zoom/center the residues now on display.
For complete list of the effects of the return, enter, shift, ctrl, and option keys, see Summary: Action of Key Modifiers. Although you can get along in DeepView with minimal use of these keys, you will find that they greatly improve the ease of selecting and displaying desired portions of the model.
The DeepView Select menu provides other commands for selecting.
Select: All <return> heading: side The menu command selects all groups, <return> displays them, and clicking the side heading adds the side chains.
Tools: Compute H Bonds In the blink of an eye, DeepView finds and displays all potential hydrogen bonds in the molecule, including those involving side chains and hetero groups. DeepView displays hydrogen bonds as green dashed lines. You will learn more about this feature later.
Select: Secondary Structure: Helices <return> You should see only the alpha-helical regions of lysozyme, with hydrogen bonds shown. Turn off all side chains. Look around to confirm that the segments shown are helical. Confirm that most of the hydrogen bonds are from the carbonyl oxygen of residue n to the amide nitrogen of residue n + 4. Notice the Control Panel: only the residues in helices are red. This allows you to take further action on the selected groups, such as coloring them, as you will see in the next section.
Select: Seconday Structure: Strands <return> You should see only strands of beta pleated sheet. Notice the characteristic pattern of hydrogen bonds in the strands. Which strands are parallel, and which are antiparallel, to each other? Illustrate this by drawing an arrow diagram of the sheet.
Display: Show H Bonds You will find that this command has a checkmark to its left, which means it is turned on. By selecting it, you turn it off, and remove the hydrogen bonds from the display.
Notice the other Select menu commands. Can you select and display only the residues whose side chains carry positive charge (so-called basic residues)? Can you select and display only the histidine residues and their side chains? (Look at the submenu that pops up when you choose Select: Group Kind.) How many histidines are present in lysozyme?
Wind: Layer Infos The Layer Infos window provides information about the display. Note the Sel heading at the top of the far right column. This column shows the number of groups currently selected. Again select the basic residues, and notice the number selected under the Sel heading. Now select acidic residues. Compare the number of acidic and basic residues in lysozyme. Would you expect the isoelectric pH or pI of lysozyme to be above or below pH 7? (It's around pH 10, because basic side chains outnumber acidic ones). Put away the Layer Infos window by clicking on its close box, the small square in its upper left corner.
Select only groups NAG 201-203 and then press return and help. You should see tri-NAG only. Manipulate and get to know this trisaccharide structure.
Another powerful selection tool lies at the top of the graphics window. It is the ninth button from the left, showing an eye and a circle. Click this button. In the message space just beneath the movement icons, DeepView instructs you to pick an atom. Click the nitrogen atom (blue) on the center ring (NAG 202). A dialog appears: Click to darken the first button (add to display), type the number 8 in the box and click OK. You have added to the display all groups having at least one atom within 8.0 angstroms of the atom you picked. (You may need to click the side heading in the Control Panel to add the side chains.) This is a nice feature for focusing your attention on specific atoms and their neighbors. Notice that DeepView adds these groups to the display but does not select them. Other buttons in the dialog allow you to select the neighbors or to display only the neighbors. In addition, Select:Visible Groups allows you to change the current selection to include all groups on the screen.
More commonly, you might want to display all groups within a specified distance of the selected groups. Accomplish this selection as follows:
First, select and display only NAG 201-203.
Select: Neighbors of Selected aa... In the dialog, type the number 4.5 in the box and click OK. You have added to the display all groups having at least one atom within 4.5 angstroms of any atom in NAG 201-203.
Here is yet another powerful means of selection. Select, display, and center the whole model with side chains.
Display: Show H-Bonds (You computed H-bonds earlier, and DeepView still remembers them.
Now select NAG 201-203 (select only -- do not remove other groups from the display).
Display: Show Only H-Bonds From Selection Display: Show Only Groups With Visible H-Bond <help> With this simple set of commands, you have limited the display to the tri-NAG inhibitor and residues to which it is hydrogen bonded.
Select: Visible Groups Select: Inverse Selection heading: ribn <help> Now you should have a model of lysozyme in which tri-NAG and its hydrogen-bonded groups are shown in wireframe, with all the rest of the model shown as a ribbon.
The command Select: Inverse Selection is a handy way to select only the groups not currently selected. Any time you want to carry out an operation on everything except the current selection, remember this command.
Turn off the ribbon by shift-clicking any checkmark in the ribn column.
Now click anywhere in the empty chain column (left column of Control Panel), and press<return> and <help>. The whole model reappears. Because there is only one chain in this model, a click in the empty chain column selects the full model.
