How to Install Your Scripts into the Chime Template

This document assumes that you have saved some portable scripts with RasMol. Instructions for saving such scripts correctly are given in a separate document Preparing RasMol-Saved Scripts for Teaching, available at http://www.umass.edu/microbio/chime/prsswc/prssft.htm

1. Copy all of the "minimal template" files into the same folder where your scripts and PDB files are located. In addition to your scripts and PDB files, you need ONLY these files, which are the "minimal template" file set:

     right-a.htm          main-cpt.js
     right-b.htm          2atoms.pdb
     right-c.htm          click.spt 
     left.htm             cs_amphi.spt
     twoframe.htm         cs_atgc.spt
     rightutl.htm         fontsize.htm
     rightucs.htm         up.gif
     cpk_cs.htm           down.gif
     vertemp.htm          [fontsize.js]
     font_how.htm         
   
     instruct.htm         contents.htm
     2frmcont.htm         mousesum.htm
     2fc-how.htm
   

   Only the files right-a.htm, right-b.htm, right-c.htm need to be customized (one or more of these depending on how many pages you need for your presentation). The others need no changes.

   [File fontsize.js is no longer needed but is provided to assist in installing font-size control into existing presentations.]

   The files grouped at the bottom are not needed unless you wish to put your presentation on the web. In this case, you'll also need to customize contents.htm.

2. In Netscape Navigator 3.01 (or later), use the File, Open File menu to open the file twoframe.htm. All other files are linked to this file. You can use this window to test your progress as you follow the steps below.

3. Editing HTML files. For the next several steps below, you will need a text editor to modify some HTML (HyperText Markup Language, web page) files. (Macintosh: Word or SimpleText. Windows: Notepad or Wordpad.) In Word or Wordpad, it is essential that (when given any other options) you save the files as plain text = ASCII text = MS-DOS text. Run the text editor program of your choice, and use its File, Open menu to open the file right-a.htm. Use it to make the changes described in the next few steps.

4. Title. In the file right-a.htm, change the title of the page to reflect your topic. The title is near the top of the file, between big tags, like this:

   <big>
   Your Page A Title Goes Here
   </big>
   

   Save the modified file (as ASCII or MS-DOS text!). Now, reload the document in Navigator to see the change. (Click the Reload button at the top, or right-click in the right frame, and select reload frame.)

5. Your first button/view. In the file right-a.htm, each block which looks like the sample below generates one square button. Each button will produce a view from one of your scripts. You need to change only the three parts in boldface. These are explained in detail in the next three steps below.

   <!-- Here is the first button -->
   <script language='javascript'>
   	button("script a010.spt");
   </script>
   
   <!-- Substitute the name of your .spt script file above.
   Below is the 'button-label-text' -->
   
   (script file a010.spt) Your button label goes here.

   (Items between <!-- and --> are comments which you see only when you are editing the HTML; the browser does not display comments.)

6. Script filename. If you named your first script file a010.spt (a for Page A, 010 for the first script), you don't need to change the script name. If you used a different filename for your first script, rename your script file to a010.spt; or edit a010.spt to the name of your script in the above HTML and then save the file right-a.htm. Do not use a master script for a Chime button! Use one of the scripts you saved directly from RasMol for each Chime button.

   If you edited the script name in right-a.htm (and saved it as plain text), switch to your Netscape window and press Reload. Now try your script button.

   Troubleshooting. If your view does not appear when you press the button, you first need to be sure your script runs in RasMol. If you have problems getting your script to produce the view in RasMol, use the troubleshooting section in the document Preparing RasMol-Saved Scripts for Teaching.

   If your script runs OK in RasMol, but not when you press the button in Netscape, here are the possible reasons and solutions:

   • Each time you press a button, but no image appears, Chime "hangs" and must be restarted. If you forget to restart it, it won't work even after you fix the original problem! Press the Reload button on Navigator; this restarts Chime. Reload Chime after every button failure.

   • You have given the wrong script name in the file right-a.htm, in the button(...) statement which creates the button. The name in right-a.htm and the actual script filename must match. Use portable filenames for your scripts, and especially avoid including embedded spaces. Solution: rename the script file or use the text editor to fix the script filename in right-a.htm so that the two script filenames match. [Win95: make sure you are not hiding file extensions. In your Win95 working folder, pull down the View menu and select Options. Select the View tab. Check "Show all files" and uncheck "Hide MS-DOS file extensions", then click OK.]

   • The load command in your script specifies the absolute pathname of the PDB file in RasMol, which never works in Chime. Solution: use Notepad, Wordpad or MS Word (Macintosh users see note at end of document*) to remove the absolute path prefix from the load command in your script, and change the PDB filename to lower case. For example, change

     load pdb "C:\M1\RASDAT\SCRIPTS\DNA-RSS\1D66.PDB"
     

     to

     load pdb "1d66.pdb"
     

     Be sure to save the script as plain/MS-DOS text.

   • The PDB file needed by your script is missing from your working folder. Solution: copy the PDB file into the working folder.

   • Your PDB filename ends in .ent instead of .pdb. Some websites end their atomic coordinate filenames with .ent instead of .pdb. The .ent works fine in RasMol, but .ent filenames won't work in Chime. Solution: rename your atomic coordinate file to end in .pdb and similarly change the name in the load-command line of your script(s).

7. Label. Change the button-label-text, for example (see above) "(script file a010.spt) Your button label goes here.", to describe the image your script creates when the button is pressed.

8. Color Keys. When your view uses the CPK color scheme, you can show the color key by including this:

   <script language='javascript'>
       chonp_key();
   </script>
   

   A comment in right-a.htm lists additional forms of CPK color keys which are pre-programmed.

   You may also wish to color key words in the text you add to right-a.htm so they match the relevant parts of the view. An example in right-a.htm includes:

   <font color="#FF8080">
   protein chain A</font>,
   

   Change for example FF8080 to the color which makes your button-label-text match the color of the structure it describes. These colors are represented as three hexadecimal values, each with two digits; in this case, FF 80 80. The 3 values represent the intensities of Red, Green, and Blue (RGB) on a scale of 0-255 (0-FF hexadecimal). See the separate document RasMol/Chime Color RGB Values www.umass.edu/microbio/rasmol/rascolor.htm for lists of RGB values and further explanation. This is excerpted from the RasMol Reference Manual (as revised in late June, 1997, http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#chcolours). You may use several colors for different parts of one button-label. See, for example, the second button in right-a.htm.

   More than 256 color names are defined in Netscape. So, for example, you can say

   <font color="white">

   However, except for white and black, it is difficult to match the color names to the colors used by RasMol. This is why we recommend using hexadecimal RGB values. For example, Netscape's "green" is much darker than RasMol's because Netscape expects to put it on a white background while RasMol expects to put it on a black background.

9. Continue by adding second, third, ... buttons, and additional pages. For your second button, repeat the process of matching the script filename in the second button(...), inserting button-label text and color keys (all in right-a.htm). And so forth for the third and additional buttons/views.

   You can have as many or as few buttons/views per right-frame page as you wish. Delete unnecessary buttons, or cut and paste to add new buttons to provide one button per script.

   When changing topics, you can link to a new right frame page, for example right-b.htm, right-c.htm, .... Create additional such files by copying earlier ones. At the bottom of each file, link to the next one by editing the name of the file shown in bold:

   <a href="right-b.htm">Next Topic</a>

   You should now be able to display your entire script sequence in Netscape with Chime, starting from twoframe.htm.

10. Web delivery. If you wish, you can put your presentation on the web simply by copying the files to your institution's web server.

    First, however, you will have to change the PDB filenames in all of your scripts' load commands to lower case (see Saving portable scripts). Web servers will not recognize an upper case PDB filename (e.g. 1D66.PDB); only a lower case name (e.g. 1d66.pdb) will be served with the correct MIME type targeted to Chime.

    It would be best to create a new folder on the server for the files, since eventually you may have several groups of images all using the same filenames twoframe.htm, left.htm, right-a.htm etc. This will work provided each set is in a different folder on the server. Contact your server administrator for details.

11. Getting your server configured for Chime. If your presentation works from local files, but not from the web server, the problem is the configuration of the web server. Ask your server administrator to configure the server for the following MIME types: ".pdb" must be served as "chemical/x-pdb", ".spt" as "application/x-spt", and ".js" as "application/x-javascript". Also, ".htm" must be served as the same MIME type as ".html".

12. Putting the best foot forward. For presentation on the web, you probably should start with instruct.htm instead of twoframe.htm. This in turn goes to an alternative form of twoframe.htm, 2frmcont.htm, which starts with a table of contents. If you use this startup sequence, you will need to edit the file contents.htm to reflect your presentation.

13. This template assumes that all your scripts are RasMol-saved scripts. If you wish to utilize manually-created scripts, things can get considerably more complicated. In that case, be sure to consult the Guide to "Movie" Script Creation for RasMol and Chime, http://www.umass.edu/microbio/rasmol/makescrp.htm and also the various resources at the UMass Chime site, http://www.umass.edu/microbio/chime.

Feedback to Eric Martz.