Welcome to the CHIMEShell home page

What is CHIMEShell?

Briefly, CHIMEShell is a package of html files that allows one to put together a presentation of a protein or nucleic acid, using the CHIME plug-in to Netscape. You can include a "story" with buttons that the reader can press, but the reader can also rotate the molecule and issue his or her own commands. Very minimal understanding of writing WEB pages or plug-in tags is needed.

How do I get CHIMEShell?

You can download the latest version here, packaged in various formats. The contents of the Shell is platform-independent - works on Mac or PC. But the folder structure has been packaged and compressed, so that you can download and then expand the package on the Mac or PC.
Documentation is provided in the downloaded package. Double-click on index.html or StartHere.html.

Available formats (choose one):

CHIMEShell.sit Mac Stuffit Archive 312K
CHIMEShell.sea Mac self-expanding stuffit archive 420K
CHIMEShell.exe Windows Self-expanding 416K
CHIMEShell.zip Windows/Mac Zip-compressed 320K

Frequently asked questions

How do I embed static pictures in my "story"?

You use the following HTML command:

in which "MyPicture.jpg" is a JPG format file sitting in the same directory as your Story.html file. GIF format files (MyPicture.gif) also work just fine.

How do I get the molecule positioned properly?

In either CHIMEshell or Protein Explorer, rotate, translate and zoom to the desired view. Then type at the command line: view show. The scrolling window will provide the command needed to get this view: view set followed by a series of numbers. Copy this into a script for a button to set this view.

How do I view 2 structures simultaneously?

For side-by-side viewing of 2 structures, construct your presentation by editing the files in the CHIME2 folder. If you want to start your presentation with one structure (struct.pdb) and go on to make some points about a second structure, you will need to have a button which loads the second structure. Here's an example: put pdb file 1lih.pdb in the presentation directory edit story.htm to include the following button: <embed type="application/x-spt" width=12 height=12 button=push target="struct" script="zap;load '1lih.pdb';script '1lihReset.spt'"> Load 1lih This button will load 1lih.pdb, and also run the script 1lihReset.spt, which can be made by editing the reset.spt file to get a nice initial view for 1lih.

Can I prepare my presentation on a PC and then run it on a Mac or vice versa?

The format is identical and therefore computer-independent. All the files are simply text files, that you will run with Netscape, and thus should work on either a Mac or a PC. So you can edit your presentation on both types of computers. Before you do your final presentation you should test it -- ideally it will work on both systems since people will try it on the Web from either system.

How do I make a link pop up a new window?

<A HREF="http://www.chem.umass.edu" target="newwindow">click here for new window</A> The key thing here is the target="newwindow" addition to the standard link syntax. The name "newwindow" can be replaced by any name of your choosing, but subsequent calls using that name will go to that window (not a new one) - this can be used to advantage. Use different names in each call to be sure that truly new windows are opened.

Is there a quick way of writing a series of commands to get the desired view of my molecule?

You can use the "copy Chime script" command in the MDL menu to record a series of commands as a script. For example, pull up your protein in Protein Explorer or ChimeShell and execute the commands needed to display it as desired. Then click on "MDL" (lower right corner of the graphics window) -> Edit -> Copy Chime script. This will copy all of the commands you have executed since starting PE or ChimeShell into the clipboard. Paste the clipboard contents into a new file in simpletext. Delete the first 2 lines which relate to loading the pdb file, and save as myscript.spt. Alternatively, you can select and keep only the last in the series of commands you have executed to create subsequent views.

How do make a button that moves my molecule for the viewer (eg a slow rotation or zooming in on an active site)?

Use the command: move x y z zz rx ry rz s t

where x y z = degrees of rotation, zz = zoom, rx ry rz = translate, s = slab, and t = time (sec) it takes to do the move.