Teaching from RasMol-Saved Scripts

This version is INCOMPLETE. Check the web for a finished version.

Provided for the NSF Educational Molecular Visualization Workshops at UMass, Amherst, Eric Martz, PD.
http://www.umass.edu/microbio/rasmol/workshop.htm

If you are reading a paper version of this document, it is also available at http://www.umass.edu/microbio/rasmol/trs-spts.htm
Software, molecules, and visualization help is at the RasMol Home Page, http://www.umass.edu/microbio/rasmol

What this document is about.
Installing RasMol so it can find your scripts and PDB files.
Troubleshooting your installation.
Ensuring that your scripts will be portable!
Save scripts of desired views from RasMol, then play them back!
Optional:
Manually type script calls into a master script, with a text editor.
Add echoed captions to the master script.
Gather several master scripts into a super-master script.
Install your scripts in a web page with Chime plus buttons.
Add color keys and descriptive text.

What this document is about.

For an introduction to RasMol, see the Quick Start at http://www.umass.edu/microbio/rasmol/rasquick.htm.

This document assumes that you already know how to obtain PDB files of the desired molecules (http://www.umass.edu/microbio/rasmol/whereget.htm ), and to use RasMol to get the views you need of these molecules for teaching purposes. (By a "view" we mean a particular representation, color scheme, orientation, and magnification of a molecule.)

This document explains how to save the views you wish to show your class, and how to play them back smoothly in the correct order. It also explains how to deliver these views through the Internet/Web via Chime.

Enabling RasMol to find your scripts and PDB files.

Create a new folder to receive your saved scripts. Put the needed PDB files (or copies of them) in this folder.

Now you must install RasMol so that this folder is RasMol's working/local directory. Otherwise it will not be able to find either the scripts or the PDB files.

On the Macintosh, the RasMac application (not an alias to it!) should also be dragged into this folder before running it. (Other methods may work under just the right circumstances, but sooner or later will fail for a variety of technical reasons. Therefore we strongly recommend the above method.)
For Windows 3.1/NT 3, make a separate RasWin icon to run your scripts. In Program Manager, select the RasWin icon, then use the File menu to Copy the icon (putting it wherever you wish). Now, with the new icon selected, use File, Properties (i) to change the name of this icon to "RasWin Scripts", and (ii) to change the Working Directory to the folder containing your scripts. Always run RasWin from this icon when you plan to save or run scripts.
For Windows 95/NT 4, copy the RasWin application (not a shortcut!) into your script folder. To force a copy (rather than the creation of a shortcut), hold down the Shift key before you drag and drop the RasWin icon into the scripts folder. Alternatively, if you prefer to make a shortcut to RasWin in your scripts folder, you must change the "Start-in" folder for this shortcut. Right-click on the shortcut icon and select Properties, then Shortcut, then change the Start-In folder to be that containing your scripts.

Troubleshooting your installation.

To test your installation, run RasMol and use its File, Open menu to open one of the PDB files in your scripts folder. If you do not see the PDB file on the open menu, here are the possible reasons:

You are running a copy of RasMol which was not installed as instructed above, and hence is looking in the wrong folder. It is easy to get confused when you have more than one RasMol icon in different folders. Solution: quit ALL running RasMol's, and restart RasMol from the correct icon installed as above.
Windows (any version): your PDB file's name does not end in ".pdb". Solution: rename your PDB file to end in ".pdb". See also the section below on portability.
Windows 95/NT 4 only: Your PDB file appears to have a name ending in ".pdb" but it really doesn't. Windows 95 loves to fool you. Run Windows Explorer (from the Start menu, Programs section). Pull down the View menu and select Options. Make sure that "Hide MS-DOS file extensions" is NOT checked, then click OK. Now use Explorer to display the folder containing the PDB file. Depending on how the file was downloaded or handled, it may have inadvertantly received a name such as "1d66.pdb.txt" for example. If "hide extensions" was checked, you can't see the real name. Solution: Uncheck "hide extensions" and then rename the file.
The PDB file is empty. One possibility is that you attempted to save the file from Netscape before it finished downloading and it may have no content at all. Check
Macintosh only: the PDB file has no signature. This occurs when you use Netscape 3.01, and force downloading of a linked PDB file by holding down the Option key when you click on the link. Solution: download a copy of FileBuddy from any shareware web site. Drop the PDB file on FileBuddy. If the type and creator (signature) are shown as ???? and ????, the file has no signature. Change the type to TEXT and the creator to RSML (both upper case), and click on save.
???On the mac, if it has the wrong signature and name does not end in .pdb, does the file appear on the open menu?

Ensuring that your scripts will be portable!

There is a crucial trick for making RasMol-saved scripts portable. (or on Windows 3.1 systems, in RasMol's working directory; or on Windows 95 systems, RasMol's Shortcut Properties, Shortcut, Start-in folder). Now, instead of using RasMol's File menu to Open your PDB file, type the command load "filename.pdb". The result of this trick is that scripts you save from RasMol will be portable, provided that you always have the scripts themselves, the requisite PDB files, and RasMol (or its working/start-in folder) all in the same folder.

Technical details: You don't have to read this paragraph to use the above trick. If you open the PDB file from RasMol's menu, it remembers the full absolute pathname of the file, and saves it into the script. When you put the script in a different folder or system, it can't find the PDB file. The 'load' command, given without a PDB filename path prefix, causes RasMol to save the PDB file 'bare', with no path prefix.

If you forget to 'load' your PDB file, the symptom will be that your script will run in the original RasMol folder, but will not run when the script + PDB files are in a different folder or system, and will not run in Chime. You can fix this easily by using a text editor to delete the absolute pathname prefix from the load command in the 7th line of each RasMol-saved script. For example, change


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


load pdb "1d66.pdb"

Lower case filenames are recommended. Failure to change the filename to lower case will cause problems on case-sensitive operating systems such as unix. It is also strongly recommended that you name all PDB files with a name not longer than 8 characters (use only letters, digits, and the underscore character) plus ".pdb" for compatibility with Windows 3.1. This will be important, for example, should you give copies of your scripts to others who use Windows 3.1 to run from their local hard disks.

Save scripts of desired views from RasMol, then play them back.

Save each view into a script file by typing the RasMol command save script filename, where filename is a filename of your choice, for example for your first view, it could be view1.spt.

Typing the command script filename into RasMol plays back the script.

Create a Master Script.

Suppose you have saved a dozen scripts from RasMol, and now you want to be able to show them quickly to a class, without typing script filename for each one (and without remembering all the filenames!).

You'll need a text editor. Simple-text is recommended on the Macintosh; Notepad is recommended on Windows95. The goal is to save your typed commands into a plain text file, not a formatted word processor file. (If you use Wordpad, be sure you save files as plain text!)

Create a master script file (let's call it master.spt) containing a list of script call commands, each followed by a pause command. An example is mast-p.spt, a master script file which calls four scripts showing views of one chain of the Gal4 transcriptional regulatory protein. The command script mast-p.spt causes RasMol to show the first image. You can now rotate, zoom, translate, and slab with the mouse. When any key is pressed, the first pause is released, and the second image comes up, and so forth.