User:James D Watson/Using Jmol: Difference between revisions
New page: ==Introduction to Jmol== Jmol is a commonly used molecular graphics viewer. The aim of this tutorial is to provide you with an introduction to some of the common manipulations to help you ... |
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==The Menu== | ==The Menu== | ||
In this section we will be looking at the structure of the haemoglobin protein (PDB entry ). The display shown here clearly shows the folding patterns of the polypeptide chains, and the arrangement of the chains with one another. However, it does not give you an accurate picture of the shape of the molecule, nor of the significance of the bound ligand. In this tutorial we will use the menu options to change the display in order to highlight these different aspects. Throughout this section, we will represent selections using the Jmol menu in '''''this style'''''.<br/> | |||
<br/> | |||
First, access the Jmol menu... | |||
Access the Jmol menu by clicking on the word "Jmol" in the lower right corner of the structure display area. The main panel of the Jmol menu will appear. (To close the menu without using it, click anywhere else in the structure window). | |||
...then Select... | |||
After accessing the main panel of the Jmol menu, move the cursor over the word Select. In the Select submenu that appears, click on All. The whole menu will disappear, and Jmol will perform the task of selecting all the atoms in the structure--but the display will not change (yet). | |||
...then Render. | |||
Access the main menu again. This time, place the cursor over Render to see its sub-menu. In the Render submenu, move the cursor to Atoms and then click on 100% vanderWaals. The menu disappears, and Jmol changes the display so that each atom in the structure is a solid sphere. This rendering is commonly called "spacefill". ("vanderWaals" describes a certain type of spacefill.) | |||
Check your results | |||
In this tutorial, you can check that your menu selections work as expected by clicking the "View Animation" links, which will trigger the display to show what the menu selections should have achieved. Compare your current results with this display: | |||
Here are the same instructions written in a shorthand way: | |||
Select | All | |||
Render | Atoms | 100% vanderWaals | |||
From here on, we'll write all the menu commands in the shorthand style. To return to the original display, here are the commands: | |||
Select | All | |||
Render | Atoms | Off | |||
The Jmol Menu | |||
Removing things from view | |||
What if you only want to see the protein, without the pigments? | |||
Select | Hetero | Ligand | |||
Render | Bonds | Off | |||
The pigments (which are ligands of this protein) were displayed as bonds only, so turning off the bonds turned off the display of the pigments altogether. | |||
Now let's redisplay the pigment, this time as a "ball and stick" model, and also with the atoms colored by element. | |||
Select | Hetero | Ligand | |||
Render | Scheme | Ball and Stick | |||
Color | Atoms | Scheme | Element (CPK) | |||
Zoom in using the mouse to get a better look at the atoms of the pigments. | |||
Showing specific amino acids: | |||
Sometimes, you may want to look at a certain amino acid or a type of amino acid in a molecule. For example, some proteins are stabilized by disulfide bonds, which are covalent bonds formed between two cysteine side chains. Three disulfide briges are present in the protein insulin. First, we'll look at the overall structure of insulin. | |||
As you see, insulin is quite a small protein. To the see disulfide bonds, use the Jmol menu in the sequence below: | |||
Select | Protein | All | |||
Render | Atoms | Off | |||
(Don't worry, it's supposed to disappear!) | |||
Render | Structures | Cartoon | |||
Select | Protein | By Residue Name | CYS | |||
Render | Bonds | 0.3 Å | |||
Color | Disulfide Bonds | Yellow | |||
Note that that the cartoon and stick renderings would have been hidden by the spacefilled atoms if you had neglected to turn them off. This is because the current rendering choice is not automatically turned off when another choice is selected; each rendering style is controlled individually, so multiple display styles of the same atoms are possible. | |||
You can also change the display of disulfide bonds under Render | Disulfide Bonds, but note that they must be part of the currently selected set of atoms to be affected by the change. | |||
Inverting selection | |||
What if you want to change the display of everything except the cystines? | |||
Select | Protein | By Residue Name | CYS | |||
Select | Invert Selection | |||
Color | Cartoon | Orange | |||
The Jmol Console | |||
Jmol can also be controlled using a command language. Knowing even a few simple commands can useful. To access the Console, use the Jmol menu: | |||
Console... | Open | |||
A small window, the Jmol Console, will appear at the upper left corner of your screen. A cursor will be blinking in the lower part of the window. This is where you can enter commands. | |||
Type the following command: | |||
select all | |||
and click the "Execute" button on the Console. Jmol writes a few things into the upper part of the Console window after executing the command, including the number of atoms selected. | |||
Now type: | |||
color purple | |||
and click the "Execute" button again. | |||
And finally, type: | |||
spacefill 100% | |||
and click "Execute". | |||
The Console allows very powerful control of Jmol with the command language. You can see a listing of Jmol commands at the Jmol interactive scripting documentation page (opens a new window). | |||
Now that you are more familiar with Jmol, click below to move to the section on protein secondary structure. | |||