If you are resuming the tutorial after a break, start your desktop copy of RasMol, arrange the windows as in section 1, and open 3b5c. Restrict the view to residues , mainchain only. Turn on hydrogen bonds. Display: Spacefill Rotate this model to view it end-on.
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Much of the following material was taken verbatim with permission from a tutorialwritten by Gale Rhodes of the Univ. In view of time constraints, I have removed much of the original tutorial. A detailed RasMOL manual is available at. The name RasMol comes from raster display of molecules.
Raster is a type of computer display especially useful for showing solid surfaces. Download a PDB file. Start Firefox. In the pop-up menu, choose " save to disk " and save the file 1CYO. By default the file will be downloaded onto the desktop. Getting started. This information includes a list of the most frequently used RasMol commands. Any time you would like to know more about a command, just type help followed by the command.
This help is somewhat sketchy, but is quick and handy. When RasMol starts, it always shows a wireframe model of all the atoms in the protein and in any other molecules such as cofactors or inhibitors that are included in the PDB file. Now you see only the alpha carbons of the protein, connected by straight lines. Try some of the other Display commands. End by displaying the backbone model. This command colors alpha helices hot pink, beta strands yellow, beta turns blue, and other parts of the model light gray not my choice of colors!
This command selects only the hetero non-protein groups in the file, excluding the water molecules that are frequently included in crystallographic models. Nothing happens until you issue another command.
NOTE that commands affect only the currently selected atoms. Also notice that you do not need to bring the Command Line window to the front in order to type commands. RasMol displays a ball-and-stick model of the selected atoms. Notice that this command does not affect the protein chain, because it is not selected. RasMol colors the selected atoms according to widely used chemical conventions: carbon is light gray, nitrogen is light blue, oxygen is red.
Notice again that the menu command affects only the currently selected atoms. Click on any alpha carbon of the protein and watch the command line. This is called "picking" an atom.
When you click on an atom in the Main Window, RasMol identifies it. You should see something like this:. This tells you that you clicked on the alpha carbon CA of residue 81 in cytochrome b5, which is a proline. RasMol calls a residue a "group", and a nonprotein portion of the molecule, including a water molecule, a "hetero".
Listed below is the sequence of commands you have used so far. You can use this sequence to give you a quick overview of any macromolecule for which you have a PDB file, and to reveal any hetero groups cofactors, inhibitors, water, and so forth that are present in the file.
The sequence is. Colours: CPK. Next you will learn how to manipulate the model. You can rotate it, move translate it to a different part of the screen, and zoom in or out. Note: if the mouse seems to get stuck in this mode, press the alt key with the left mouse button.
Translate X or Y: middle button and drag. Picking, Selecting, and Restricting. It does not alter the display of the selected atoms. Subsequent commands will affect only the selected atoms. RasMol draws residues 64 through 72 as a stick model. Try rotating the model. RasMol is still rotating about the center of the whole molecule.
Fix this as follows:. Now find the lysine residue at one end of the helix. Click on its alpha carbon. RasMol will now rotate the model around this atom. This resets picking to identify picked atoms without changing the centering of rotation. The last command is another way to change the center of rotation. Notice the syntax of the atom expression that follows the word center. An atom expression describes a particular atom or set of atoms.
This expression for a single atom consists of the abbreviation of the residue arg , followed -- without a space between -- by the residue number 68 , a period, and the atom name ca for alpha carbon. An atom name is always preceded by a period. The previous command also contained an atom expression: RasMol is pretty picky about the syntax of these expressions, so take careful note when you encounter them.
You can use these expressions in select and restrict commands as well. For more information about expressions, type help expressions, help primitives , and help examples.
The side chains disappear. You have restricted the selected atoms to residues 64 through 72, and to the mainchain atoms of the protein. Mainchain is one of many "sets" that you can specify in RasMol commands. For a listing of the names of other sets, type help sets return. RasMol draws dotted lines for all the main-chain hydrogen bonds of currently selected residues.
Rotate this model to view it end-on. Notice that stick models make protein structures appear very open and empty, but even an isolated helix is quite densely packed. This returns the full backbone to the screen, centers rotation on the center of the whole model, and returns it to the original orientation.
The last four commands are useful when you get lost and need to redisplay everything and get your bearings again. This command removes all residues except those in pleated sheet sheet is another set. Cartoon displays show sheet strands as arrows pointing toward the C-terminal end of the chain. Now you see the whole protein as a cartoon. This is a vivid display that is easy to interpret. Now you see the heme prosthetic group in its cartoon-protein binding site. Now you see the heme as a ball and stick model surrounded only by atoms that lie within 7.
The restrict within and select within commands are powerful tools for directing your attention to specific interactions within macromolecules.
Click on one atom then another. A dotted line appears between the atoms, along with the distance between the atoms in angstroms. This sequence resets picking to the default and removes all measurement lines and labels. This sequence selects only the sidechains of hydrophobic residues, and colors them yellow. The hydrophobic set is another set of atoms you can use in select commands. To see the names of other colors, type. This sequence selects all carbons in the hem and colors them cyan.
The question marks stand for unspecified characters. The selection hem. RasMol's Main Window should now display a wireframe model of cytochrome b5.
Colours: Structure This command colors alpha helices hot pink, beta strands yellow, beta turns blue, and other parts of the model light gray not my choice of colors! Colours: CPK RasMol colors the selected atoms according to widely used chemical conventions: carbon is light gray, nitrogen is light blue, oxygen is red.
Much of the following material was taken verbatim with permission from a tutorialwritten by Gale Rhodes of the Univ. In view of time constraints, I have removed much of the original tutorial. A detailed RasMOL manual is available at. The name RasMol comes from raster display of molecules. Raster is a type of computer display especially useful for showing solid surfaces. Download a PDB file. Start Firefox.
RasMol Version 2.6-beta-2 Reference Manual