Molecular Modeling on the Web using Chime

INSTRUCTIONS

Last updated 02/02/2001

Note:  You can view Chime files on the web using Netscape in any public access computer at CSB/SJU.  To see them on your own computer (either PC or Mac), you have to download (for free) the plugin from MDI, the company that distributes it.  Select the link below to get the download:

MDL Information Systems, Inc

I.  Using Chime commands to modify the renedering of the molecule:

The rendering of  molecules can be changed in several ways.    For simple changes, the easiest way is to right click on the actual molecule, and a new selection of commands will pop up. You can then select an appropriate command with a click of the left mouse button. A check will apear by scommand indicating that you have selected it. The important command options are shown below along with a brief comment in red about the use of some of them.

Chime Commands

File

• Save Molecule As - it would seem like you could save a rendering of your molecule this way but it doesn't seem to work for me.

Edit

• Copy Chime Script - This might be useful if you went to someones else's Chime page (several are referenced below) and see something particularly interesting for which you would like to use the commands. You could then copy the Chime script and paste it into your page1.html document from the HTML editor of Front Page and see if it works for you. It's worth a try, but if you are trying to copy a bunch of Java code, I don't think it will work.

Rotation

Display - Can't do much more than what's available with buttons from the command window.

• Wire
• Stick
• Ball
• Space Fill
  • Van der Waals Radii
• Backbone
• Ribbon
• Strands
• Cartoon

Options

• Display Hydrogens - Very useful since X-Ray structures don't have hydrogens since they don't have enough electrons to diffract x-rays. However, by placing them in, H bonds make more sense since they will come from a H on a N or O, and not from an N or O to a N or O.
• Display Hydrogen Bonds
• Display Disulfide Bridges - Useful to see how many and where the disulfides are
• Dot Surface
  • Van der Waals
  • Conally Surface - This is the water-accessible surface of the molecule, as we encountered in Quanta/Charmm.
• Labels
• Sprout Hydrogens - same as display H's above, I think.
• Stereo Display - Believe it or not, you can see these images in 3D if you can cross you eyes. This command splits the image into two which if viewed with crossed eyes, or flayed eye, will result in the appearance of a 3D image.

Color -allows you to color code by something other than the originary red for O, blue for N, white for H, etc, CPK color system.

• Monochrome
• CPK
• Amino Acid
• Shapely
• Group
• Chain
• Temperature
• Structure

Select - This is the most imporant of all these commands because it allows you to select only certain parts of the display for showing. You will have to experiment on your own with this, but just looking at the commands allows you to see the possibilities. Notice that you can select all, invert a selection (i.e. show everything you didn't select), or hide a selection.

• Select All
• Mouse Click Action
• Highlight Selection - this must be clicked to see the results of your selection process
• Invert Selection
• Hide
  • Hide Selected
  • Hide Not Selected
• Change Color
  • (to a whole series of possilbe colors)
• Modify Selection Mode
  • Replace Selection
  • Add to Selection
  • Add common to Selection
  • Subtract from Selection
• Chain
  • A
  • B
• Residue
  • (alll the amino acids in a file are listed)
• Atom
  • (select different atoms - alpha C, H, O's etc)
• Hydrogen
• Nonhydrogen
• Hetero
  • Hetero
  • Solvent
  • Nonsolvent
  • Water
  • Ions - this should be great for displaying a bound ion
  • Ligand - this should be great for displaying a bound ligand
• Protein
  • Protein
  • Amino
  • Large
  • Medium
  • Small
  • Alpha Carbon
  • Backbone
  • Bonded
  • Buried
  • Helix
  • Sheet
  • Side Chain
  • Surface
  • Turn
  • Acidic - great to show areas of localized charge density
  • Acyclic
  • Aliphatic
  • Aromatic
  • Basic - great to show areas of localized charge density
  • Charged
  • Cyclic
  • Cystine (disulfide bond)
  • Hydrophobic - great to show areas of localized hydrophobicity
  • Neutral
  • Polar
• Nucleic Acid
  • Nucleic
  • DNA
  • Bacbone
  • AT
  • CG
  • Purine
  • Pyrimidine
• Display List
  • Create Molecular Surface - This takes a while to generate, and doesn't offer a significant advantage over van der Waals or Conolly surfaces.
  • Color
    • Electrostatic Potential - Should be great to show how differences between regions of net postive charge and regions of net negative charge give rise to a net electrostatic potential
    • Lipophilic Potential - Should be great to show how differences between regions of net high hydropathy and regions of net low hydropathy give rise to net hydrophobic moment
    • (various colors listed)

You can change the view of the molecule by right-clicking on the molecule, and then using the commands that follow. Here is an example of how to do that.

Lambda repressor:DNA complex: with built-in Chime commands.

Remove the protein and display just the DNA in space filling mode in a way to visualize the major and minor groves by right-clicking on the molecule frame, and then selecting the following  :

• Choose Select, Nucleic Aicid, Nucleic Acid, to select just the nucleic acid.
• Choose Select, Hide, Hide not Selected, to view only the nuclei acid.
• Choose Select, Nucleic Acid, Backbone, in preparation to change the color of the sugar-phosphate backbone.
• Choose Select, Change Color, Red, to change the color of just the backbone to red.
• Choose Select, Nucleic Acid, Nucleic Acid, to select the entire DNA molecule again.
• Chose Display, Space Fill, Van der Waal, to see the dsDNA colored coded in space-fill rendering. You should not be able to easily differentiate the major and minor grove.
• Choose Select, Protein Protein to prepare to alter the rendering of the protein
• Choose Display, Wireframe to see the protein in wire frame mode. The rendering of the DNA should not change.
• Choose Color, CPK, to change the coloring of just the protein to the regular coloring scheme.

II.  Creating your own Web-based modeling tutorials

The example above shows how unwieldy it can be for the user to alter the rendering of the molecule in a desired way.  It would be much better to be able to place buttons for all these commands in a frame adjacent to the molecule frame.   In that way you could create a sequential set of buttons which when clicked would display important features of the molecule is an easy, step-wise fashion.  This is what you will do for your final Web-based modeling project. Select the link below, which will display the same DNA-protein complex as you justed modified with Chime commands,  to see how much easier it is for the user to be able to select from a series of preprogamed step by clicking buttons to change the rendering of the complex.

Lambda-Repressor Complex with Self-Programmed Buton Commands  - A Presentation Template

To facilitate making tutorial, I've created two kinds of templates.   One, used above for the lambda-repressor complex, is useful for oral presentation (such as for CH351).  The other is better for self-guided, web-based tutorials (such as for your final project), as shown below. 

Beta Structure - A Web-Based Tutorial Template

Creating/Modifying Web Pages

It is easy to create your own personalized Presentation and Tutorial Template.  the simplest way is to copy the files used to created the above examples, and modify them with an HTML web presentation program, such as  Microsoft Front Page 2000, which is available on the network.  Click on the Windows start button, and then select Network Programs, Web Publication Tools, and then Front Page 2000.  When it opens, you can open your own web files stored on the web server by selecting File, then Open Web, and then at the bottom typing in http://www.students.x.csbsju.edu/usrname, where x is the first initial of your first name.  You can open web files on your network m: drive by selecting File, Open, and then selecting the Computer File icon in the new window.  Select  that icon, and follow prompts to load files from your M: drive or floppy drives.  If you would like to load Front Page 2000 on your own PC, you can purchase it from IT Services for $5.

When you save web  files, save them in your M: drive. If you use Front Page, do not save them on the front page server, because chime files don't run if stored there. Select File, Save As, and a new window opens. At the bottom right of the window you will see two icons, one for the WWW and the other for a computer file. Select the computer file and then follow prompts to save your file to your M: drive.

I have posted all the files required for the Presentation and Tutorial Templates in public folders at:

Public Folders\All Public Folders\\Academic\Chemistry\Henry Jakubowski\01CH331.  There you will find 3 folders:

• Prot - this contains files for a Tutorial Template
• ProtDNA - this contains files for a Presentation Template which displays a complex of DNA and protein
• ProtProtLig - this contains files for a Presentation Template which displays a complex with two protein chains and a ligand

You should copy these files to your m: drive.  Then, if the Chime Plug-in is loaded on your computer, all you have to do to click on the template.html file (or the .pdb file or the molecule.html file) and you should see the structures displayed.

What kinds of files are in the templates?

Presentation Template: 

There are 3 kinds of files required to make a presentation template:   commands.html (or.htm), molecule.html,  and template.html.  The commands and molecule files will be displayed as the left and right hand frames of the template file when the template file is opened wiht Netscape, as shown below.  A molecule structure will appear in the molecule.html frame if you have the Chime Plug in loaded into your browser (which will happen automatically if you are working in a public access   lab) and if you have a .pdb file available as well. 

Web Tutorial Template

There are 4 kinds of files required to make a presentation template: molecule.html, commands.html, page1.html, and template.html.  The  molecule and page1  files will be displayed as the top and bottom left hand frames of the template file and the commands file as the right side frame of the template fiile when the template file is opened with Netscape, as shown below.  A molecule structure will appear in the molecule.html frame if you have the Chime Plug in loaded into your browser (which will happen automatically if you are working in a public access  lab) and if you have a .pdb file available as well. 

Editing molecule.html:

Load the file(from your m: drive) into Front Page. At the bottom window you will see tabs. Click the HTML tab to actually edit the code for the page. All you have to do it change the name of the pdb file in the page. Use the find command to find xxx.pdb. Simply change this name to the name of the file you downloaded form the web. Remember it must have a .pdb extension.  It is very important that when you put the name of the pdb file into your molecule.html file, or any other file, that you put it in with the correct capitalization.  The program is case sensitive.  Make sure that when you write file names in any of these files, that they have the same capitalization as the actual file name.  (For example, if your pdb file name is 1A3h.pdb, you must write it that way any time you place in the .html files.

Edting commands. html:

If you use the commands.html file from a Tutorial Template folder (as in Beta Structure - A Web-Based Tutorial Template), you don't have to change this file.  However, it is easy to change to make it specific to your protein, as I did for the commands.html file for the Presentation Template.  (As in Lambda-Repressor Complex with Self-Programmed Buton Commands  - A Presentation Template)   You can insert these commands directly into your HTML document, which will allow a user to change the rendering of the molecule by clicking a button in the document window.    For example, if you wish to add this button and command to your commands window:

Display DNA

you can copy the HTML code (by opening the command.html file with FrontPage, selecting the HTML tab at the bottom left, and copying the code for that button and command:

<p><embed SRC WIDTH="12" HEIGHT="12" align="baseline" border="0" type="application/x-spt"
button="push" target="MOLECULEFRAME"
script="
refresh;
select all;
wireframe off;
spacefill off;
dots off;
cartoon off;
select nucleic;
wireframe on;
spin on;
">
<font FACE="Arial" COLOR="#FFFFFF"><strong>Display DNA</strong></font></p>

To change what the button will do, you need to learn what the commands like wireframe off; mean.  The best way to do this is to look at the files I've placed in the public folders and try them on your own system.   Another way to learn these is through the Chime tutorial links or viewing (and copying) the html source fropm other cool Chime web sites.

CHIME LINKS FROM THE WWW:

Go to the links below for ideas and additional information:

HELP

MDI Systems, Inc. - the parent company that distributes Chime.  From here you can get downloads, learning and development information, and a list of great Chime sites.

Another Chime Tutorial from ?

GREAT SITES USING CHIME

World Index of BioMolecular Tutorials in Chime

The Online Macromolecule Museum at Kenyon College

WWU Virtual Molecular Model Kit - Teaching Organic Structures on the Web

Molecular Models for Biochemistry

3D Structural Database of Pharmaceuticals

A Chime tutorial on VSEPR theory

A Chime tutorial on Coordination Chemistry