Using Chime Command-Script Files in Protein Explorer's Project Folder with Microsoft Internet Explorer (PE/IE)

The Chime (and RasMol) commands "load" and "script" request atomic coordinate files (PDB files, "molecules", .pdb) and files of command scripts (filenames ending .spt) for processing by Chime. These are processed correctly in Netscape 4, but not in PE/IE (PE requires Chime 2.6SP3 in IE 5.5SP2. See Browsers compatible with PE -- ignore the warning that your browser is incompatible.)

Since "load" and "script" commands request files, in PE, they are permitted only when you have set a Project Folder. The instructions below deal with methods for using "load" and "script" commands in PE when a Project Folder has been set.

This document explains how to run script files of rendering commands (select, display/hide, color) in PE/IE from your Project Folder by excluding "load" commands from the script files.

Presently, PE does not provide a template for constructing presentations -- this is under development. The old template (released before PE was created) does not work in IE. (It works well in Netscape.) Therefore, for the time being, you're on your own in using any scripts you develop with the help of PE.

It is also possible to send commands to Chime in a javascript string, instead of a script file. This method has fewer problems, but requires more programming expertise. In order to implement PE in IE, some script files were converted to script strings. (If you are technically minded, you may be interested in Implementation of PE in IE).

PE/IE is also unable to process "delay" or "move" commands in script files (but it can handle these in script strings, see above). These bugs place severe limitations on the use of scripts in PE/IE that can be avoided by using Netscape 4. If, nevertheless, you wish to use script files in PE/IE, read on.

In IE, a Chime "load" or "script" command stops execution of the script -- commands following the "load" or "script" command don't execute. If, however, the script is a string (not a file), the remaining commands get executed following the next "load" or "script" command received. Here is an example that will make this clearer. Needless to say, this makes for great confusion. (There appear to be further bugs, not described here, that affect script files containing "load" commands followed by rendering commands.)

Partial Solution. You must separate "load" commands from the commands that render (display and color) the molecule. There are two ways to issue load commands:

Having loaded your molecule, you can now manually enter a second command to run a rendering script. Rendering command-script files appear to work provided they don't include a "load" command. Also, .spt files cannot include any script commands themselves (to call script subroutines) since these would kill execution.

Rendering scripts must avoid "delay" and "move" commands because these also kill execution. Thus, animations and movies are precluded from script files, but can work in script strings (as demonstrated in PE's Animation capability).