KE0026 Biochemistry Labs

Computer lab: Introduction to molecular graphics

The purpose of this lab is to learn how to use a graphics program called Swiss PDB Viewer, SPV for short. This is a program for visualising protein molecules, and will be used in more detail in later labs. 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.

The SPV manual contains everything you need to know about the program, so whenever you have problems, this is the place where you find the answer.

Getting started:
In order to see something you need to give the coordinates for a protein to the program. Coordinates are usually written in files called pdb-files.
The pdb-files of most of the structures solved so far are collected in a large data-base called the PDB. In the Structure gallery to this course some proteins and their pdb-files can be found. The structure gallery is under "self study resources" in the blue menu on the left.

->Download two different structures from the structure gallery. You can choose any two you'd like to see.
To do this, you go to the page for each structure, and with the pointer in the Chime window, hold down the mouse button and select "File" | "Save Molecule As.." from the popup menu.

->Now find the program and start it. A window with different pulldown menues should now appear. This is called the graphics window.

Opening a pdb-file in SPV:
To see a protein you must open up its pdb-file in SPV.
->Go to this side 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 one of the two files you downloaded earlier. Click OK on any dialogs that might appear. You can close the inputlog window that opens.

One trick you should learn now is how to center your molecule in the window.
->Press = on your keyboard to center the molecule.

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 side of the SPV manual to see how to rotate, translate or zoom the proteins.
If you have a three button mouse, try to press each of the buttons and move the mouse.

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

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

Now look at the control panel. You have a lot of columns present. Most important, you have a list of all the amino acid residues present in your protein.
Two important things: when an amino acid is couloured 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!!
->Try clicking on one of the amino acids and then press 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. 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 gets selected.
What do you think the letters stand for?

->What does the colums "Show" and "Side" mean?

Tips:
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? That means that you have more than one chain in your protein. If you click on one of these letters, all the amino acids belonging to that chain get selected.

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.
->Now open up the second pdb-file you saved, and center both of your molecules.
How do you select wich protein to look at in your control panel? What happens if you check "can move" for only one of them?

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.

->Use the select menu to look at:
all the alpha helices your protein contains.
Then look at your beta sheets.
Look at all the polar amino-acids you have.
Finally check out how many phenyl-alanines 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 Ca atoms of your amino acids.
->Choose the slab alternative. What is it good for? Rotate your molecule and see what happens.

Colour menu:
This is the menu for colouring your molecule, or more often parts of your molecule. It is very well discribed in this section of the SPV manual. Read that!

->Play around with the colours, and try the different alternatives in the menu. When can it be useful to use them? Try colouring different parts of the protein in different coulours. A very useful option is to colour after secondary structure. Do that!
Worth noticing is the option "other colour...". Here you can choose the colour 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 colour a specific amino acid, or a group of amino acids.
Do you notice that your colour selection only applies to the protein you have selected to view in the control panel? In this way you can colour your two proteins in different ways, so that you more easily recognise them.
Try to do that!

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.

The graphics window:
This is the window that first appeared when you started up the program. You can see many buttons in this window with pictures explaining what they are for.
Go through all the buttons and try to figure out what they mean. You should be able to do this just by clicking at the button and follow the instructions in the window. Don't be afraid to try! It doesn't matter if you screw up the whole structure, you're going to throw it away anyway at the end of the lab!! To "unclick" a button, just hit "esc" on your keyboard.

Now you have (hopefully) gone through some of the features of this program. Now just do this last exercise and show it to the lab-teacher.
->Colour one of your two molecules after secondary structure. Look only at the ca-atoms and nothing else.
->For the other molecule: Look only at the secondary structure, that is, those amino acids with either an h or an s in front of them. Try to colour all of the different strands and helices in different colour.
Now move only one of your molecules so that it is as close as possible to the other one without touching it.

Did you make it? Great, now call the teacher and show what you just did!

Lab index

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