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

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=== Bound ligands and solvent ===

Displaying the entire protein as spacefill spheres gives a better impression of the actual shape of the protein. In this case the four subunits are clearly packed together with little space between them. It is also evident that there are a number of small molecules bound to the protein surface. These are often solvent molecules (water, deuterium, etc) or artefacts of the crystallisation process (glycerol, etc), but they can also represent substrate mimics, inhibitors and cofactors.

Displaying the entire protein as spacefill spheres gives a better impression of the actual shape of the protein. In this case the four subunits are clearly packed together with little space between them. It is also evident that there are a number of small molecules bound to the protein surface. These are often solvent molecules (water, deuterium, etc) or artefacts of the crystallisation process (glycerol, etc), but they can also represent substrate mimics, inhibitors and cofactors. In the example shown there are a number of water molecules which is confusing the identification of any ligands. To remove these atoms:

In the example shown there are a number of water molecules which is confusing the identification of any ligands. To remove these atoms:

'''''Select | Hetero | All Water'''''

'''''Main | Style | Atoms | Off'''''

This leaves the remaining bound small molecules (<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint2/1'>"Check Section"</scene>). Explore the structure some more to confirm the identity of these tightly bound molecules as the haem groups (''Hint: Toggle off the spinning and click on the Jmol window. Moving your cursor over an atom should provide a pop-up window identifying that atom/residue'').

Now let's focus in on a haem group to see how it interacts with the protein. To restrict the view to just the ligand molecules perform the following menu choices:

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

'''''Style | Atoms | Off'''''

'''''Main | Set picking | Select molecule''''' then click on the two PO4 groups and any three of the haem groups

'''''Style | Atoms | Off'''''

'''''Main | Set picking | Center'''''

~~Now let's focus in on a haem group to see how it interacts with the protein. To restrict the view to just the ligand molecules perform the following menu choices:~~

~~'''''Select | Protein | All'''''~~

~~'''''Style | Atoms | Off'''''~~

~~'''''Main | Set picking | Select molecule'''''~~

~~Then click on the two PO4 groups and any three of the haem groups~~

~~'''''Style | Atoms | Off'''''~~

~~'''''Main | Set picking | Center'''''~~

Click on the orange atom in the centre of the haem (iron) and the molecule should centre there - try rotating to see the effect.

A different type of view with bonds shown as sticks and atoms shown as smaller spheres) can be obtained using the following menu choices:

A different type of view with bonds shown as sticks and atoms shown as smaller spheres) can be obtained using the following menu choices:

'''''Main | Set picking | Select molecule''''' (then click on the haem group to be viewed)

'''''Main | Select | None''''' (this resets the selection to nothing)

'''''Style | Atoms | 25% van der Waals'''''

'''''Main | Set picking | Select molecule''''' (then click on the haem group to be viewed)

'''''Style | Bonds | 0.20A'''''

'''''Style | Atoms | 25% van der Waals'''''

'''''Style | Bonds | 0.20A'''''

It is known that the haem group in haemoglobin is bound tightly to a histidine residue (the proximal histidine). To identify this residue use the following set up selections:

'''''Main | Select | None''''' (this resets the ~~selction~~ to nothing)

It is known that the haem group in haemoglobin is bound tightly to a histidine residue (the proximal histidine). To identify this residue use the following set up selections:

'''''Select | Protein | By residue name | His''''' (the number in brackets gives the occurrence of that residue type in the protein)

'''''Main | Select | None''''' (this resets the selection to nothing)

'''''Style | Atoms | 25% van der Waals'''''

'''''Select | Protein | By residue name | His''''' (the number in brackets gives the occurrence of that residue type in the protein)

'''''Style | Bonds | 0.20A'''''

'''''Style | Atoms | 25% van der Waals'''''

'''''Style | Bonds | 0.20A'''''

The screen will now fill with all the histidines in all chains, but this is cluttered. It is evident that there are two histidines particularly close to the haem group (one above and one below). To restict the view to these two groups and the haem we will use the picking tool followed by "view selected only":

The screen will now fill with all the histidines in all chains, but this is cluttered. It is evident that there are two histidines particularly close to the haem group (one above and one below). To restict the view to these two groups and the haem we will use the picking tool followed by "view selected only":

'''''Main | Select | None''''' (this resets the selction to nothing)

'''''Main | Select | None''''' (this resets the selction to nothing)

'''''Main | Set picking | Select group'''''

'''''Main | Set picking | Select group''''' - then click on the haem group and the two nearby histidines.

~~Then~~ click on the haem group and the two nearby histidines.

'''''Main | Select | Display Selected Only'''''

'''''Main | Select | Display Selected Only'''''

A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode (<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint3/1'>"Check Section"</scene>). Rotate and look at the view. The histidine closest to the haem group is the proximal histidine and the other is the distal. What do you notice about the plane of the haem ring? Why is this relevant to the structure of deoxyhaemoglobin?

A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode. "Check ~~HERE~~"

This concludes a basic introduction to manipulating structures in Jmol to identify interesting features using the menu choices. This exercise is by no means exhaustive, so please feel free to explore the menus and see the effects they have.

Rotate and look at the view. The histidine closest to the haem group is the proximal histidine and the other is the distal. What do you notice about the plane of the haem ring? Why is this relevant to the structure of deoxyhaemoglobin?

This concludes a basic introduction to manipulating structures in Jmol to identify interesting features using the menu choices. This exercise is by no means exhaustive, so please feel free to explore the menus and see the effects they have.

==The Jmol Console==

Jmol can also be controlled using a command language based on the commands from RasMol. This is effectively a scripting system and the use of a handful of simple commands can replace the use of a greater number of menu choices. To access the Console, use the Jmol menu:

   '''''Main | Console | Open'''''

A small popup window will appear. This is the Jmol Console, in which a cursor will be blinking - this is where you can enter commands. For a full list of commands please go to the Jmol homepage and look up the documentation at [http://jmol.sourceforge.net/ http://jmol.sourceforge.net/].

To quickly illustrate the power of the Jmol console, open the console in the Jmol window to the right and type the following commands (use "Ctrl+Enter" after each command to start a new line for the next command in the series):

<ul>

<li>select all

<li>color cpk (colours by atom type)

<li>restrict *b (restricts the selection to chain b)

<li>centre selected

<li>select [HEM]&*b (select all HEM groups from chain b)

<li>spacefill 50% (display selected residues as 50% spacefill)

<li>color purple

<li>center selected

<li>select HIS &*b (select all Histidine residues from chain b)

<li>color green

<li>spacefill 50%

<li>restrict HEM,his63,his92

</ul>

Once entered, click on the "Execute" button on the Console - you will see a number of things being written into the upper part of the Console window followed by the display changing. You can also press enter or click on "Execute" at any stage to see the effect each command has.<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_final_script/1'>"Click here to see the end result"</scene>.

You can see how if you build up a series of useful scripts you can rapidly display different proteins in the same way (or highlight the same aspects). It should also be noted that you can select a list of commands from a text editor and copy-paste them into the Console command area as a single script to be run. Please feel free to play with different commands - but remember: all commands are only performed on the last selected atoms!

==References and Acknowledgements==

This tutorial was inspired by the "Interactive Concepts In Biochemistry" Structure Tutorials published by John Wiley & Sons ([http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/structure.htm http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/structure.htm])

Jmol: an open-source Java viewer for chemical structures in 3D. [http://www.jmol.org/ http://www.jmol.org/]

RasMol: Biomolecular graphics for all [http://www.openrasmol.org/ http://www.openrasmol.org/]. Original reference: Roger A. Sayle and E. James Milner-White, Trends in Biochemical Sciences 20(Sept):374-376, 1995.

Key reference for PDB entry 4HHB:

~~The Jmol Console~~

G.Fermi et al. (1984). The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. J Mol Biol, 175, 159-174. PubMed id: 6726807.

~~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~~.

@@ Line 58: / Line 58: @@
 === Bound ligands and solvent ===
+Displaying the entire protein as spacefill spheres gives a better impression of the actual shape of the protein. In this case the four subunits are clearly packed together with little space between them. It is also evident that there are a number of small molecules bound to the protein surface. These are often solvent molecules (water, deuterium, etc) or artefacts of the crystallisation process (glycerol, etc), but they can also represent substrate mimics, inhibitors and cofactors. <br/>
 <applet load='4hhb' size='400' frame='true' align='left' caption='Haemoglobin molecule - het groups' scene='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint1/1'/>
-Displaying the entire protein as spacefill spheres gives a better impression of the actual shape of the protein. In this case the four subunits are clearly packed together with little space between them. It is also evident that there are a number of small molecules bound to the protein surface. These are often solvent molecules (water, deuterium, etc) or artefacts of the crystallisation process (glycerol, etc), but they can also represent substrate mimics, inhibitors and cofactors. In the example shown there are a number of water molecules which is confusing the identification of any ligands. To remove these atoms:<br/>
+In the example shown there are a number of water molecules which is confusing the identification of any ligands. To remove these atoms:<br/>
-'''''Select | Hetero | All Water'''''<br/>
+&nbsp; &nbsp;'''''Select | Hetero | All Water'''''<br/>
-'''''Main | Style | Atoms | Off'''''<br/>
+&nbsp; &nbsp;'''''Main | Style | Atoms | Off'''''<br/>
 <br/>
 This leaves the remaining bound small molecules (<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint2/1'>"Check Section"</scene>). Explore the structure some more to confirm the identity of these tightly bound molecules as the haem groups (''Hint: Toggle off the spinning and click on the Jmol window. Moving your cursor over an atom should provide a pop-up window identifying that atom/residue'').<br/>
+Now let's focus in on a haem group to see how it interacts with the protein. To restrict the view to just the ligand molecules perform the following menu choices:<br/>
+&nbsp; &nbsp;'''''Select | Protein | All'''''<br/>
+&nbsp; &nbsp;'''''Style | Atoms | Off'''''<br/>
+&nbsp; &nbsp;'''''Main | Set picking | Select molecule''''' then click on the two PO4 groups and any three of the haem groups<br/>
+&nbsp; &nbsp;'''''Style | Atoms | Off'''''<br/>
+&nbsp; &nbsp;'''''Main | Set picking | Center'''''<br/>
 <br/>
-Now let's focus in on a haem group to see how it interacts with the protein. To restrict the view to just the ligand molecules perform the following menu choices:
-'''''Select | Protein | All'''''
-'''''Style | Atoms | Off'''''
-'''''Main | Set picking | Select molecule'''''
-Then click on the two PO4 groups and any three of the haem groups
-'''''Style | Atoms | Off'''''
-'''''Main | Set picking | Center'''''
 Click on the orange atom in the centre of the haem (iron) and the molecule should centre there - try rotating to see the effect.
+<br/>
+<br/>
-A different type of view with bonds shown as sticks and atoms shown as smaller spheres) can be obtained using the following menu choices:
+A different type of view with bonds shown as sticks and atoms shown as smaller spheres) can be obtained using the following menu choices:<br/>
-'''''Main | Set picking | Select molecule''''' (then click on the haem group to be viewed)
+&nbsp; &nbsp;'''''Main | Select | None''''' (this resets the selection to nothing) <br/>
-'''''Style | Atoms | 25% van der Waals'''''
+&nbsp; &nbsp;'''''Main | Set picking | Select molecule''''' (then click on the haem group to be viewed)<br/>
-'''''Style | Bonds | 0.20A'''''
+&nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
+&nbsp; &nbsp;'''''Style | Bonds | 0.20A'''''<br/>
-It is known that the haem group in haemoglobin is bound tightly to a histidine residue (the proximal histidine). To identify this residue use the following set up selections:
+<br/>
+<br/>
-'''''Main | Select | None''''' (this resets the selction to nothing)
+It is known that the haem group in haemoglobin is bound tightly to a histidine residue (the proximal histidine). To identify this residue use the following set up selections:<br/>
-'''''Select | Protein | By residue name | His''''' (the number in brackets gives the occurrence of that residue type in the protein)
+&nbsp; &nbsp;'''''Main | Select | None''''' (this resets the selection to nothing) <br/>
-'''''Style | Atoms | 25% van der Waals'''''
+&nbsp; &nbsp;'''''Select | Protein | By residue name | His''''' (the number in brackets gives the occurrence of that residue type in the protein)<br/>
-'''''Style | Bonds | 0.20A'''''
+&nbsp; &nbsp;'''''Style | Atoms | 25% van der Waals'''''<br/>
+&nbsp; &nbsp;'''''Style | Bonds | 0.20A'''''<br/>
-The screen will now fill with all the histidines in all chains, but this is cluttered. It is evident that there are two histidines particularly close to the haem group (one above and one below). To restict the view to these two groups and the haem we will use the picking tool followed by "view selected only":
+<br/>
+The screen will now fill with all the histidines in all chains, but this is cluttered. It is evident that there are two histidines particularly close to the haem group (one above and one below). To restict the view to these two groups and the haem we will use the picking tool followed by "view selected only":<br/>
-'''''Main | Select | None''''' (this resets the selction to nothing)
+&nbsp; &nbsp;'''''Main | Select | None''''' (this resets the selction to nothing) <br/>
-'''''Main | Set picking | Select group'''''
+&nbsp; &nbsp;'''''Main | Set picking | Select group''''' - then click on the haem group and the two nearby histidines.<br/>
-Then click on the haem group and the two nearby histidines.
+&nbsp; &nbsp;'''''Main | Select | Display Selected Only'''''<br/>
-'''''Main | Select | Display Selected Only'''''
+A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode (<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint3/1'>"Check Section"</scene>). Rotate and look at the view. The histidine closest to the haem group is the proximal histidine and the other is the distal. What do you notice about the plane of the haem ring? Why is this relevant to the structure of deoxyhaemoglobin? <br/>
+<br/>
-A checkbox should appear and you will have one haem group and two histidines displayed in "ball-and-stick" mode. "Check HERE"
+This concludes a basic introduction to manipulating structures in Jmol to identify interesting features using the menu choices. This exercise is by no means exhaustive, so please feel free to explore the menus and see the effects they have.<br/>
+<br/>
-Rotate and look at the view. The histidine closest to the haem group is the proximal histidine and the other is the distal. What do you notice about the plane of the haem ring? Why is this relevant to the structure of deoxyhaemoglobin?
+{{Clear}}
-This concludes a basic introduction to manipulating structures in Jmol to identify interesting features using the menu choices. This exercise is by no means exhaustive, so please feel free to explore the menus and see the effects they have.
+==The Jmol Console==
+Jmol can also be controlled using a command language based on the commands from RasMol. This is effectively a scripting system and the use of a handful of simple commands can replace the use of a greater number of menu choices. To access the Console, use the Jmol menu:
+<br/>
+&nbsp; &nbsp;'''''Main | Console | Open'''''
+<br/>
+A small popup window will appear. This is the Jmol Console, in which a cursor will be blinking - this is where you can enter commands. For a full list of commands please go to the Jmol homepage and look up the documentation at [http://jmol.sourceforge.net/ http://jmol.sourceforge.net/].<br/>
+<br/>
+<applet load='4hhb' size='400' frame='true' align='right' caption='Haemoglobin molecule' scene='User:James_D_Watson/Using_Jmol/Haemoglobin_start2/1'/>
+To quickly illustrate the power of the Jmol console, open the console in the Jmol window to the right and type the following commands (use "Ctrl+Enter" after each command to start a new line for the next command in the series):<br/>
+<ul>
+<li>select all
+<li>color cpk (colours by atom type)
+<li>restrict *b (restricts the selection to chain b)
+<li>centre selected
+<li>select [HEM]&*b (select all HEM groups from chain b)
+<li>spacefill 50% (display selected residues as 50% spacefill)
+<li>color purple
+<li>center selected
+<li>select HIS &*b (select all Histidine residues from chain b)
+<li>color green
+<li>spacefill 50%
+<li>restrict HEM,his63,his92
+</ul>
+<br/>
+Once entered, click on the "Execute" button on the Console - you will see a number of things being written into the upper part of the Console window followed by the display changing. You can also press enter or click on "Execute" at any stage to see the effect each command has.<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_final_script/1'>"Click here to see the end result"</scene>.<br/>
+<br/>
+You can see how if you build up a series of useful scripts you can rapidly display different proteins in the same way (or highlight the same aspects). It should also be noted that you can select a list of commands from a text editor and copy-paste them into the Console command area as a single script to be run. Please feel free to play with different commands - but remember: <b>all commands are only performed on the last selected atoms!</b><br/>
+<br/>
+{{Clear}}
+==References and Acknowledgements==
+This tutorial was inspired by the "Interactive Concepts In Biochemistry" Structure Tutorials published by John Wiley & Sons ([http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/structure.htm http://www3.interscience.wiley.com:8100/legacy/college/boyer/0471661791/structure/structure.htm])<br/>
+<br/>
+Jmol: an open-source Java viewer for chemical structures in 3D. [http://www.jmol.org/ http://www.jmol.org/] <br/>
+<br/>
+RasMol: Biomolecular graphics for all [http://www.openrasmol.org/ http://www.openrasmol.org/]. Original reference: Roger A. Sayle and E. James Milner-White, Trends in Biochemical Sciences 20(Sept):374-376, 1995. <br/>
 <br/>
+Key reference for PDB entry 4HHB:<br/>
-The Jmol Console
+G.Fermi et al. (1984). The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. J Mol Biol, 175, 159-174. PubMed id: 6726807.
-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.