Provided for the
NSF Educational Molecular Visualization Workshops
at UMass, Amherst and Long Island U, Brooklyn NY, Eric Martz, PD.
If you are reading a paper version of this document, it is
also available at http://www.umass.edu/microbio/rasmol/2fc-how.htm
Software, molecules, and visualization help is at the RasMol Home Page, http://www.umass.edu/microbio/rasmol
Thanks to Craig Martin and the students in his class on Biomolecular Structure, as well as pioneering efforts by Tim Maffett, David Marcey and Henry Rzepa which inspired the approach taken here.
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
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.
<big> Your Page A Title Goes Here </big>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.)
(Items between <!-- and --> are comments which you see only when you are editing the HTML; the browser does not display comments.)
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:
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.
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). Hexadecimal equivalents of some colors are given in the RasMol 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.
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.
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.
Feedback to Eric Martz.