User:James D Watson/Using Jmol: Difference between revisions

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==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'''''.

In this section we will be looking at the structure of the human deoxy-haemoglobin protein (PDB entry 4HHB). 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 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'''''.

~~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~~).

In order to access the Jmol menu click 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~~ Render.

It is vitally important to understand that all actions are performed on what was last selected. If the display does not change as you expect it to, doubly check what you have selected, make the selection again and redisplay. To select something via the main panel of the Jmol menu, move the cursor over the word '''''Select'''''. This will bring up a selection of sub-menus, click on '''''All'''''. The whole menu will disappear, and Jmol will perform the task of selecting all the atoms in the structure, please note that the display will not change yet.

In order to change the display you need to "render" your selection. To render, access the Jmol main menu again and place the cursor over '''''Render''''' to see its sub-menu. Move the cursor to '''''Atoms''''' then click on '''''100% vanderWaals'''''. The menu will disappear and the display will change so that each atom is represented as a solid sphere (commonly called "spacefill").

Try this for yourself and if you want to check that your menu selections worked correctly you can click on the "Check Section" links. These will change the Jmol image to show what the menu selections should have resulted in.

From now on we will represent successive menu selections in the following way:

'''''Select | All'''''

'''''Render | Atoms | 100% vanderWaals'''''

Will repeat the steps taken above.

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

@@ Line 28: / Line 28: @@
 ==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/>
+In this section we will be looking at the structure of the human deoxy-haemoglobin protein (PDB entry 4HHB). 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 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/>
 <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...
+<applet load='4hhb' size='400' frame='true' align='right' caption='Haemoglobin molecule'/>
-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).
+In order to access the Jmol menu click 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).<br/>
+<br/>
-...then Render.
+It is vitally important to understand that all actions are performed on what was last selected. If the display does not change as you expect it to, doubly check what you have selected, make the selection again and redisplay. To select something via the main panel of the Jmol menu, move the cursor over the word '''''Select'''''. This will bring up a selection of sub-menus, click on '''''All'''''. The whole menu will disappear, and Jmol will perform the task of selecting all the atoms in the structure, please note that the display will not change yet.<br/>
+<br/>
+<br/>
+In order to change the display you need to "render" your selection. To render, access the Jmol main menu again and place the cursor over '''''Render''''' to see its sub-menu. Move the cursor to '''''Atoms''''' then click on '''''100% vanderWaals'''''. The menu will disappear and the display will change so that each atom is represented as a solid sphere (commonly called "spacefill").<br/>
+<br/>
+Try this for yourself and if you want to check that your menu selections worked correctly you can click on the "Check Section" links. These will change the Jmol image to show what the menu selections should have resulted in.<br/>
+<br/>
+From now on we will represent successive menu selections in the following way:
+'''''Select | All'''''
+'''''Render | Atoms | 100% vanderWaals'''''
+Will repeat the steps taken above.<br/>
+<br/>
-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