Swiss-PdbViewer basics

Reading material:   The DeepView manual (also available as a PDF file here) and the SPDV FAQ.

Goals: to learn how to use Swiss-PdbViewer to view and analyze proteins.

Coordinate files and the PDB

In order to make (and see) a picture of a particular protein, you need to give its "coordinates" to a viewing or "graphics" program. It's a lot like drawing a graph: you need to have the data points to make the picture, although many different kinds of pictures can be made using the same set of data, depending on what things you want to show. The coordinates are really just a list of x,y,z positions for each atom of a structure; they are usually collected in a text file called a "pdb file". The pdb files for most of the structures that have been experimentally determined have been deposited in a large database called the PDB (Protein Data Bank). When you want to look at a particular structure, you can usually find that coordinate file at the PDB.

So, let's get a structure that we can use to show some basic concepts in protein structure, that of a cellulase.

Downloading a PDB file
One example of how you might download a PDB file is provided by using this link. If you are on a Mac, download the file with the right button of the mouse ("Save link target as"); save it someplace sensible, and remember where that is! Same basic idea, if you are on a PC...

You could also download 1CEL directly from the PDB. To do this, enter the "1CEL" code in the search box at the top of the PDB page, then hit the carriage return. If you get a list, choose the file you want (1CEL) by clicking on the code to the left. To the right, choose "Download Files", then "PDB File (Text)".

Note that if you download the file the second way, there will be two molecules; just turn the second (B) molecule off later (in Swiss-PdbViewer). The two molecules are present because of some technical reasons in the crystallography, i.e. this protein is not a dimer!

The program
To actually make pictures of the protein, you will use a program called Swiss-PdbViewer (SPV or SPDVfor short, now also called DeepView, just to keep us confused). This program should be under Start/Allprograms/kursprogram/SwissPdbViewer if you are on a PC at the BMC. It should be found on the Dock if you are on a Mac at the BMC; if it is not there, you should put it there. If you can't find it anywhere, you can always download it from the GlaxoSmithKline site; lots of folks get this (free) program for their home or other computers!

Many of you have used this program before, but you may need are refresher. In any case, the more you learn about the program during this lab, the easier it will be in the future; so take the time to play around a bit, and explore the different possibilities of the program. And don't forget, the SPV manual has lots of useful information.

Opening a PDB file in SPV
So, start the SPV program by double-clicking on its icon.

A window with different pulldown menus should now appear. This is called the graphics window. Go to this page of the SPV manual and read the first part on this page on how to open a pdb file, the part called: loading one molecule. Then open the 1CEL.pdb file you downloaded a little while ago. Click OK on any dialogs that might appear. (You can just close the input-log window that opens.)

One trick you should learn now is how to center your molecule in the window.
->Press the 'insert' key on your keyboard to center the molecule or click on the right mouse button (if you have a Mac the = key does this; check the manual under 'Tips&Tricks').

How to rotate your molecule
See anything yet? You should be able to see your protein, centered in the window. Now if you hold down the button on the mouse and move it,your molecule will rotate. Read this page of the SPV manual to see how to rotate, translate or zoom in on the protein.
If you have a three-button mouse, try pressing each of the buttons and moving the mouse.

->Do you see which button that causes which movement? Move the two molecules around a bit to get a feel for how to view them from all different angles, how to move them to the side, and how to zoom in.

The Control Panel
This is a very important window. When you master this, more than half the battle is won!!! If it didn't appear when you opened your pdb file, you can find it under the Windows menu.
Open up the control panel, and then read this page of the SPV manual.

Now look at the control panel. You have a lot of columns present. Most importantly, you have a list of all the amino acid residues present in your protein.
When an amino acid is colored red,it is selected, when it is black, it isn't. If you press return on your keyboard, only the selected amino acids will be shown in the display window!!
->Try clicking on one of the amino acids and then pressing return.
Now select amino acids 1-10. Try also to hold down "ctrl" on your keyboard and then click on a number of amino acids that are not next to each other. Do you see that you can add amino acids to view in this way? Center the amino acids you are looking at!

In some cases there is a letter to the left of your amino acids, either an s or an h. Click on one of them and press return. What did you see?
Note that even if you only click on one h or s, all the amino acids close to this one with the same letter in front are selected.
What do you think the letters stand for?

->What do the columns "Show"and "Side" mean?
To select all the amino acids in a protein, go to the select menu and choose "All".
To mark all the selected amino acids in the "Show" or "Side" column,click on the word "Show" or on the word "Side".
To unmark all the amino acids selected for the same two columns, press"ctrl" and "shift" at the same time and click at the words.

->Do you have a capital letter in the far left column? Like A, B or C? If there is more than just A to be seen, that means that you have more than one polypeptide chain in your protein. If you click on one of these letters, all the amino acids belonging to that chain gets elected.

At the top of the panel you have a box called "visible" and a box called "can move". Try checking/unchecking them to figure out what they mean.

Select menu
Check out this page in the manual to read what you can do with the select menu.
Together with the control panel you can choose exactly what you want to look at.

->For instance, you can use the Select menu to:
Look at the alpha helices of your protein.
Look at your beta sheets.
Look at all the polar amino-acids you have.
Finally, see how many phenylalanines there are.
Don't forget to press "return" after each selection.

Display menu
From this menu you can choose what to look at in the selected amino acids.

->Choose to look at only the alpha-carbon atoms of your amino acids.
->Choose the Slab alternative. What is it good for? Rotate your molecule and see what happens.


Color menu
This is the menu for coloring your molecule, or more often, parts of your molecule. It is very well described in this section of the SPV manual. Read that!

->Play around with the colors, and try the different alternatives in the menu. Try coloring different parts of the protein in different colors. A very useful option is to color according to secondary structure. Try that!
Worth noticing is the option "other color...". Here you can choose the color you want by mixing red, green and blue (RGB). Play around a bit with this option.
Also by clicking in the box to the far right in the control panel, you can select to color a specific amino acid, or a group of amino acids.
Do you notice that your color selection only applies to the protein you have selected to view in the control panel? In this way, you can color two proteins in different ways, so that you more easily recognize them.
Try to do that, if you got the file directly from the PDB (second option above). 

Windows menu
In this menu you can choose what windows you want to have open. Look at the different alternatives. If there are any you don't understand, consult the manual.

Thanks are due to Jenny Berglund for many aspects of this exercise.

Last modified: S. Mowbray, 22 August, 2014.