Scripting Wizards for Molecule Viewing

The Scripting Wizards are a collection of JavaScript-powered web pages that guide you through the process of developing scripts to control display of molecules in the Chime and RasMol molecular viewing programs. They act as both an on-line quick reference to the commands of the Chime/RasMol scripting language, and as a menu-driven authoring tool.

System requirements

These Wizards are only supported on Netscape Navigator version 4.05 or higher. Certain features may or may not work on other browsers or versions. They have been tested on Navigator 4.50 on both Windows 98 and Macintosh PPC system 8.5 using Chime 2.0a, and with Navigator 4.05 on System 7.5.5 using chime 1.0.

These programs run noticably faster on a fast computer (a Celeron 300A at 450 MHz is pretty snappy), and may be slow over a modem connection. You must be sure to wait until each page loads clicking on options, or loading may be interrupted.

Wizard Hierarchy

The various Wizards call and send results back to each other as outlined below: 

    Chime Scripter
     /         \
AddButton   AddMolecule
     \         /
    Script Wizard
          |
  Expression Wizard

The Chime Scripter calls on the Add Molecule and Add Button wizards to create HTML tags for molecules and buttons (respectively). These tags are collected in a Code Box in the Chime Scripter window, and used to create a Preview window, to see the molecule and buttons in action. Each molecule can have a startup script that runs when it loads, to determine how it is initially displayed on the page. Buttons also have associated scripts that will be applied to the button's target molecule when the button is clicked. The Script Wizard can be called from either the Add Button wizard or the Add Molecule wizard to assist in creating these scripts.

Subsets of atoms to which script commands will be applied can be specified by "atomic expressions". The Expression Wizard assists in creating such expressions.

Example


Fe
O2
Heme
zoom

Wizard-generated code for above example

<embed src='http://www.rcsb.org/pdb/cgi/export.cgi/1HHO.pdb?pdbId=1HHO&format=PDB&compression=chime' name=1hho bgColor=#000000 display3d=backbone align=left height=70% width=70% ></embed><br> <embed type="application/x-spt" target=1hho height=16 width=16 button=toggle immediate=no script="select iron #specify atoms in iron atoms spacefill on #use van der Waals radii" altscript="select iron #specify atoms in iron atoms spacefill off #use van der Waals radii" ></embed> Fe <br> <embed type="application/x-spt" target=1hho height=16 width=16 button=toggle immediate=no script="select oxygen AND within (6.0, iron) #specify atoms in oxygen atoms AND a radius of 3.0 Angstroms of iron atoms spacefill on #use van der Waals radii" altscript="select oxygen AND within (6.0, iron) #specify atoms in oxygen atoms AND a radius of 3.0 Angstroms of iron atoms spacefill off #use van der Waals radii" ></embed> O<sub>2</sub> <br> <embed type="application/x-spt" target=1hho height=16 width=16 button=toggle immediate=no script="select ligand #specify atoms in cofactors and ligands wireframe 50 #set wireframe thickness" altscript="select ligand #specify atoms in cofactors and ligands wireframe off #set wireframe thickness" ></embed> Heme <br> <embed type="application/x-spt" target=1hho height=16 width=16 button=toggle immediate=no script="centre selected #center current selection zoom 200 #set magnification %" altscript="reset" ></embed> zoom <br>

Obtaining a local copy for use off-line

Running the Chime Scripter Wizards off-line will provide a significant performance boost over running them from a modem connection. It will also let you use the programs without being connected to the Internet. Since there are so many files involved, you can download a local copy of the entire directory as a zip file. Unzipping programs for most types of computers are widely available (at shareware.com, for example).

The help files used by the Wizards are not included in this package. For off-line use, you should download copies from their original locations on the web. If these files are saved with the correct names, they will be used as help files whenever the Wizards are run from a local hard disk. If the Wizards are used from a web server, the help files will be used from their original locations on the Net.

For off-line help on Chime/RasMol scripting commands, save http://www.umass.edu/microbio/chime/manual/chimeman.htm as a local file named "chimeman.htm"

For off-line help on Chime Embed tags, save http://www.mdli.com/support/chime/embed.html as a local file named "embed.html"

More Chime and RasMol resources

Please send questions or comments to rmhorton@attotron.com.