Workshop on Molecular Visualization for Biological Science Teaching: RasMol and Chime

University of Massachusetts, Amherst MA, June 1998
Eric Martz, emartz@microbio.umass.edu. Project Director
Chemistry Resource Center (CRC) Computer Lab, Goessman 152, Dr. Beatrice Botch, Director.
Assisted by Rashie Athukorala, Honor Glenn, Tim Driscoll, and Ken Rotondi.
Computer configuration by Frank Stolle.
Supported by the Undergraduate Faculty Enhancement Program of the Division of Undergraduate Education, NSF, and the University of Massachusetts.

If you are reading a paper version of this document, it is also available at http://www.umass.edu/microbio/rasmol/w1agend3.htm

Overview of Three Meetings and Two Intervals

Interval One: (3 weeks) Install software, locate PDB files, develop teaching plan. Help mentorees.

Day 2: Development of RasMol scripts for your classes. Optionally put your scripts into a web-ready Chime presentation.

Interval Two: (1 year) Complete implementation, incorporate into teaching, assess results.

Day 3: Report accomplishments and assessments to group. Recommend and discuss improvements in pedagogy. Software update.

1. Questionnaires. Netscape, RasMol Web Site, 9:00-9:30

2. Intro to Participants and Workshop 9:30-10:10

3. Downloading and Installing RasMol, 10:10-10:30
   * * * Coffee Break, 10:30-10:45 * * *

4. Basic RasMol: mouse, pull-down menus, 10:45-11:15

5. RasMol Commands, 11:15-12:00
   * * * Lunch! (Campus Center Room 1101) 12:00-1:30 * * *

6. Downloading molecules of your choice from Brookhaven's PDB, 1:30-2:15

7. Writing scripts for RasMol, 2:15-3:15
   * * * Coffee/Juice Break! 3:15-3:30 * * *

8. Chime, 3:30-4:00

9. Demonstration of MAGE; STING 4:00-4:30

10. Assignments for Interval 1, Discussion, Evaluation 4:30-5:00

1. Questionnaires; Netscape, RasMol Web Site, 9:00-9:30

• Fill out questionnaires.
• Login to your computer using the number on your name tag (01-40).
• Run Netscape Navigator.
• Go to the RasMol Web Site and explore it. www.umass.edu/microbio/rasmol
• Find the RasMol Manual and Bookmark it.
• Save your bookmarks to a disk.
• Disable file extension hiding (applies to Windows only).

Macintosh Login (Not applicable at home.)

• Open the Apple menu, select Server Login.
• Enter your account, which is workshop## where ## is the two-digit number on your name tag. If your number is 07, your account is workshop07.
• Enter the password bondatom.
  On the CRC Macintoshes, network login is needed only to use Word and for file sharing.

  Explore the RasMol Web Site

• Run Netscape Navigator: Apple menu, Network Applications, Netscape.
• Go to the RasMol Web Site: type this URL into the Location slot and press Enter. www.umass.edu/microbio/rasmol
• Bookmarks, Add.
• Explore the RasMol Web Site!

  Bookmark the RasMol Manual

• Find the RasMol Manual on the web site: at the main page, click on Index, then Getting RasMol or Chime and their Manuals.
• Click on the Bookmarks pull-down menu of Netscape, then on Add bookmark.

  Saving your bookmarks on a diskette to take home.

• If you have not already done so, insert the floppy disk that will retain bookmarks you wish to save.
• Pull down the Window menu of Netscape.
• Click on Bookmarks..., to bring up a Bookmarks window
• In the Bookmarks window, pull down the File menu, select Save As...
• Select the Diskette.
• Click the save button to save the file. Note: On the CRC Macintoshes, your bookmarks will remain all day. We recommend that you save them before lunch and before going home at the end of the day.

Windows Login

• Hold down Ctrl and Alt simultaneously while pressing Del to get the login window.
• Enter your username, which is workshop## where ## is the two-digit number on your name tag. If your number is 07, your username is workshop07.
• Enter the password bondatom.
• The domain must be CRC.
• Press the OK button.
  On the CRC Windows NT4 computers, login is needed for all work, since your working folder is on network drive J:.

  Disabling Windows file-extension hiding

• Do This Now! If you use Windows 95 at home, you should do this on your computer at home, too! Once you have done it, extensions will remain permanently unhidden (unless you re-hide them intentionally, not recommended).

  Either in the My Computer dialog (obtained by double-clicking on the My Computer icon in the upper left corner of the Desktop) or in Windows Explorer (found at the bottom of the Programs menu of the Start button on the task bar) pull down the View menu, and select Options... from the bottom of this menu. In the Options... dialog click on the View tab and make sure that no check appears in the box next to Hide file extensions for known file types. Our goal is to force Windows to show you complete file names, including extensions such as .pdb, .txt or .htm. Inability to see these extensions makes it difficult to name files correctly so that RasMol and Chime can use them.

  Explore the RasMol Web Site

• Run Netscape Navigator/Communicator: Open the Start menu (lower left of your screen), select Programs, Networking Applications, Communicator.
• Go to the RasMol Web Site: type this URL into the Location slot and press Enter. www.umass.edu/microbio/rasmol
• Click on the Bookmarks pull-down menu of Netscape, then on Add bookmark.
• Explore the RasMol Web Site!

  Bookmark the RasMol Manual

• Find the RasMol Manual on the web site: at the main page, click on Index, then Getting RasMol or Chime and their Manuals.
• Click on the Bookmarks pull-down menu of Netscape, then on Add bookmark.

  Saving your bookmarks on a diskette to take home.

  Note: On the CRC Windows NT4 computers, your bookmarks will disappear between logins. Therefore it is best to work from the bookmarks file on your diskette. Otherwise you will lose your bookmarks if your computer crashes.

• If you have not already done so, insert the floppy disk that will retain bookmarks you wish to save.
• Click on the Bookmarks pull-down menu of Netscape.
• Click on Edit Bookmarks..., to bring up a Bookmarks window.
• Under the File pull-down menu, select Save As...
• If the 3.5 Floppy (A:) is not immediately available in the Save in: box of the subsequent window, scroll up or down until you locate it, or click on the My Computer icon within that box to list all available destinations for your file.
• Click the save button to save the file.
• Prior to exiting Netscape save your bookmark file to retain any new links you have added. If you close and re-start Netscape, immediately select Bookmarks, Edit Bookmarks, File, Open Bookmarks File and specify the file you saved on your 3.5" Floppy Diskette (A:).

2. Intro to Participants and Workshop, 9:30-10:10

• Fill out workshop questionnaires if you have not done so, please!
• Meet the other workshop participants. (See separate list of participants with email addresses.)
• Introductory remarks and overview.

3. Downloading and Installing RasMol, 10:10-10:30

• Download and install RasMol -- see your first molecule!

• Open your working folder. Today, you'll be working on Drive J: in a folder named J:\MolVis. We'll refer to this throughout this document as your Working Folder. From your Start button, select Programs, then Windows Explorer. From here, find your working folder on J:, and display its contents. If you need help to do this, ask a TA. (If you are at home, simply create a new empty folder named as you wish.)

• Change to your Netscape window. In general, whenever you need to change to a different window, find the window you want on the task bar (at the bottom of the screen) and click on it. Another handy way is Alt-Tab. Hold down the Alt key, and while keeping it down, press and release Tab. Pressing Tab repeatedly will cycle you through the display of window icons. When you release Alt, the window currently circled will open in the foreground.

• Download RasMol. In Netscape, pull down the Go menu and select the RasMol Classic Main Page. Click on Index, then Getting RasMol, then Getting and installing RasMol, then RasWin for PC/Windows, then 32-bit RasWin. (We are using Windows NT4 in the CRC lab. At home, pick the version which matches your computer.)
• In the Save As... dialog, select your Working Folder and click Save.
• Run RasMol. Change to your Explorer window. Find the file you just downloaded, which is named rw32b2a.exe, and which has an icon of 3 gray balls ("atoms"). Double-click on this file. If a black window appears, RasMol is running! (The name stands for RasWin 32-bit version 2.6 Beta 2a. RasWin is simply the name of the Windows version of RasMol. There is another copy of RasWin named raswin32.exe, just in case we need it.)

• Verify that you have 1d66.pdb. Change back to Explorer. There should be a file in your Working Folder named 1d66.pdb. The goal is to get the RasWin program and the pdb files you need in the same folder. (If you are at home, download a starter set of 4 PDB files from RasMol Quick Start at www.umass.edu/microbio/rasmol/rasquick.htm#galore. After you have downloaded fourmols.exe, double-click on it to unzip these PDB files into your Working Folder.
• Open 1d66.pdb. Change back to RasMol's window, and use its File menu to Open 1d66.pdb (gal4 transcriptional regulator bound to DNA). The molecule should appear in the black window.

• RasMac is the name of the Macintosh version of RasMol; the two names will be used interchangeably.
• In Netscape, at the RasMol Web Site, click on Index, then Getting RasMol, then Getting and installing RasMol, then RasMac for Macintosh/PPC, finally, clicking on rmc26b2a.sit.hqx. On most Macs, downloaded files appear on the Desktop.
• The CRC Macs, like most, are configured to unpack the .sit.hqx (binhexed) file automatically, producing an .sit (StuffIT compressed) file, and then a "RasMol 2.6" folder. At home, if this doesn't go automatically, use Stuffit Expander on the .sit.hqx file to unpack it. (Stuffit Expander is shareware available from most shareware websites, e.g. www.shareware.com or www.filepile.com.)
• Delete the sit.hqx file, and the .sit file, leaving only the "RasMol 2.6" folder.
• Open your working folder User's Folder:MolVis.
• Open the RasMol 2.6 folder. Drag the RasMac application out of this folder into your Working Folder, where there should also be a file named 1d66.pdb. The goal is to get the RasMac application and the pdb file in the same folder. (Do not merely create an alias -- this won't work reliably.)
• Run RasMac. Use the File menu to Open 1d66.pdb (gal4 transcriptional regulator bound to DNA). The molecule should appear in the black window.

4. Basic RasMol: mouse, pull-down menus, 10:45-11:15

• Learn to use the mouse.
• Try out the most important menu options.

*Command is the "Apple" key. In RasMac the Option/Alt key seems to work interchangably with the Command key.

**Options, Slab mode must be turned on (checked) before the slab plane can be moved.

Important features to try out:

• Open and arrange RasWin's command-line window. Under Windows, the command-line window starts minimized. Look at the task bar (bottom of your screen), find RasMol Command Line and click to open it. Then rearrange windows so you can see both the black and white RasMol windows, black at the top, and white below it. (With Windows 3.1, use Alt-Tab to open the command-line window.)
• Click on an atom to report the atom/residue identification in the command-line window. The report appears in RasMol's white command line window.
• Try the Display menu. Try out these display representations: wireframe, backbone, sticks, ball-and-stick, cartoons.
• Try the Color menu. Try out these color schemes: CPK, group (end-to-end rainbow), chain, structure.
  The group color scheme colors chains in a spectral series from end to end. It scales the spectrum based on the highest residue number in the PDB file. Some PDB's, such as 1d66, give the waters high "residue" numbers, making the protein and DNA be mostly blue. To fix this, from the menu select Options, Hetero atoms (toggles off their inclusion in group coloring); then Colours, Group again. Alternatively, use RasMol's renumber command, which renumbers all residues. (Unless you then save pdb filename the renumbering occurs only in memory, not in the disk copy.)
• Try these from the Options menu: Slab, specular, shadows, stereo, labels.
• If interested, you can use the Export menu to export a GIF (to put images on web), or a color postscript file to print hi-res (see Martz FAQ [Frequently Asked Questions] at the RasMol Web Site, www.umass.edu/microbio/rasmol/faq_em.htm#printres ).

5. RasMol Commands, 11:15-12:00

• Learn to use RasMol's command-line window.
• Follow the separate handout titled "What can you learn about a protein or DNA molecule with RasMol?".
• Try generating an image with DNA as sticks with AT pairs blue, GC pairs cyan; protein as a chain-colored backbone, and metal ions spacefilled and CPK colored.

• In Windows, RasMol's command-line window starts minimized. Use the Win95 task bar, or Alt-Tab to open it.
• RasMol's Help menu is disabled because the built-in help is obsolete. Bookmark and use the RasMol manual on the web! www.umass.edu/microbio/rasmol/distrib/rasman.htm
• The most important commands/terms are: selection vs. restriction; hetero atoms; predefined groups of residues (e.g. hydrophobic); labeling; hbonds and ssbonds; within.

6. Downloading molecules of your choice from Brookhaven's PDB, 1:30-2:15

• Learn what a PDB file is. See www.umass.edu/microbio/rasmol/pdb.htm.
• Search for a molecule(s) of your choice at the Protein Data Bank, download the PDB file, and explore it in RasMol.

• In Netscape, go to the RasMol Web Site main page, and click on Molecules near the bottom. If you start at the Index, click on Molecules Galore, then on Molecules Galore again.
• Click on Macromolecules.
• Use PDB Lite to find molecules, and save them to your Working Directory.
• Open your downloaded PDB files in RasMol (one at at time) and explore them!

• PDB = Protein Data Bank, also a common data file format for atomic coordinate files. Each PDB atomic coordinate data file has an arbitrary unique four character identifier (digits and letters), such as 1d66, 1hho, 1hbs, 2hhd, 153d, 1pgb, and so forth.
• Other sources of molecules including micromolecules are at Molecules Galore on the web site.
• If you have time, click on a blue/linked reference within the header of a PDB file to jump to the National Center for Biotechnology Information's extremely useful WWW Entrez system. This integrates amino acid sequences, nucleic acid sequences, bibliographic references (MEDLINE), and 3D structural information in a single user-friendly interface. You can now search the National Library of Medicine's journals free at www4.ncbi.nlm.nih.gov/Entrez/medline.html.

7. Writing scripts for RasMol, 2:15-3:15

• Learn to use RasMol's save script filename command to save an instructive view of a molecule, and the script filename command to restore that view on demand, for example when needed for teaching.
• Learn to create, by hand, a simple script which plays back a series of RasMol-created scripts.
• Write, by hand, a script which applies a color scheme to any molecule loaded in RasMol.

• Save 3 scripts for 3 different views of any molecule(s). Try playing them back, one at a time, with the script command.
• Manual creation of a script to play back a series of RasMol-created scripts:
  • Suppose you have used RasMol to save script files named s1.spt, s2.spt, s3.spt. Now use a text editor to create a plain text file. (Use wordpad on Windows95/NT4, notepad on Windows3.1/NT3, simple text on Macintosh/PPC.) Name the file master.spt, and type into it:

    script "s1.spt"
    pause
    script "s2.spt"
    pause
    script "s3.spt"
    

  • Be sure to save master.spt into the folder which already contains the relevant PDB file (and on Macs, the RasMol application).
  • To play back the sequence, use the command script master.spt. The first image will appear -- rotate it, and optionally zoom it etc. When you are finished manipulating the first view, press the space bar to release the pause and run the next script. The second view will appear automatically, and so forth.
  • Of course you must have all the necessary PDB files in the same folder as the scripts (and on Macs, the RasMol application). Note that this method is suitable only if all the desired manipulations of the script-generated views can be done from the mouse/menus -- you can't type a command while master.spt is running.
  • If you ever want to kill a script while it is sitting at a pause (so it won't go on to the next view), hold down the control key and press D (Ctrl-D).

• Creating a color-scheme script applicable to any molecule:
  • Use your text editor to create a file named cs1.spt (for Color Scheme 1). Type these commands into it, and save it into your Working Folder.

    select a
    color blue
    select t
    color yellow
    select g
    color green
    select c
    color red
    select u
    color [128,0,255] # purple
    
    select (dna and backbone)
    color white
    background white
    
    echo
    echo DNA/RNA: Green, Carmine, Azure, Tweety-bird, pUrple
    echo
    

  • In RasMol, use the File menu to Close, then re-open 1d66.pdb. Now type the following commands into the command window, pressing Enter after each line:

    restrict dna
    center selected
    rotate z 90
    zoom 200
    wireframe 0.5
    script "cs1.spt"

    The script cs1.spt is independent of the molecule or representation. It will apply this color scheme to the DNA or RNA in any view of any molecule(s).

  • This scheme uses the following mnemonics for the 5 bases:

    G = Green

    C = Carmine (red)

    A = Azure (blue)

    T = Tweety bird (yellow)

    U = pUrple

    With not too much effort, you can read off the sequence!

• Notice that there are two kinds of RasMol scripts.
  1. RasMol-saved scripts created automatically using a save script filename command. These generate a single view , and can run in either RasMol or Chime.
  2. Manually typed scripts, created with a text editor by typing in commands. These can be very powerful: they can be designed to apply to any molecule, or generate multiple views.

• RasMol has serious limitations when it comes to presenting a series of views saved in scripts. It cannot back up; cannot easily jump randomly to a desired image; cannot have color keys or large fonts in the command-line 'legend' space; cannot run in Navigator as a web presentation; cannot have a hyperlinked outline structure, or independently scrolling hypertext; cannot have hardware-independent movement speed. All of these limitations are overcome by Chime (see below).

• If you move RasMol-saved scripts to other computers or folders, you will need to make a small change in each script with a text editor. The sixth line of every RasMol-saved script is a load command to open the PDB file. Unfortunately, RasMol writes the PDB filename as an absolute path, such as:

  load pdb "C:\RASDAT\SCRIPTS\DNA3P\1D66.PDB"
  

  You'll need to change this to a relative path by deleting everything in the quotes except the PDB filename, and change it to lower case giving for example:

  load pdb "1d66.pdb"
  

  Now, provided you keep the necessary PDB files in the same folder as the script(s), the scripts will work in any folder on any computer (Mac or Windows -- scripts and PDB files are platform-independent!).

• See the RasMol Web Site or the workshop handout Pedagogy of Molecular Visualization (also at www.umass.edu/microbio/rasmol/pedagogy.htm ) for more information on script-writing.

8. Chime, 3:30-4:00

• Chime is already installed on your computers -- go ahead and explore some Chime tutorials.
• Practice downloading and installing Chime so you will be able to do it at home.

• View some Chime presentations. In Netscape, from the RasMol Web Site, select Chime. Explore some of the Ready-to-run Chime tutorials.
  Installation of Chime cannot be done on the CRC Windows computers due to network security restrictions.

• Macintosh only (optional): Practice downloading and installing Chime. In Netscape, go to the source of Chime, MDL Information Systems Inc., www.mdli.com. Click on the Download button near the top, then click on Chime. Select Download Chime 1.0, the Macintosh/PPC version.

  Chime 2 is available in a beta version ONLY for Win95/NT4 (June 1998). It is installed on the CRC Windows computers. At home, if you have a Win95 computer with Navigator 4.x installed, you may try out Chime 2. (Communicator 4.04 is recommended; 4.05 has a bug!) Chime 2 has many amazing new features, including an extensive menu for selecting atoms, residues, chains, and predefined sets.