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

Eric Martz, emartz@microbio.umass.edu. Dept. Microbiology, U. Mass., Amherst MA.
Chemistry Resource Center (CRC), Goessman 152, Dr. Beatrice Botch, Director.
Assisted by Rashie Athukorala, Honor Glenn, and Tim Driscoll.
Computer configuration by Frank Stolle.
Supported by the Undergraduate Faculty Enhancement Program of the Division of Undergraduate Education, NSF, and the University of Massachusetts. Summer, 1997.

If you are reading a paper version of this document, it is also available at http://www.umass.edu/microbio/rasmol/w1agenda.htm

Overview of Three Meetings and Two Intervals

Interval One: (2-3 weeks) Install software, locate PDB files, develop teaching plan. Help mentorees.

Day 2: Pedagogy. Implementation of teaching plan with technical help.

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

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

1. Questionnaires, Intro to Participants and Workshop 9:00-9:40

2. Netscape, RasMol Classic Main Page, 9:40-10:10

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. Chime, 2:15-2:45

8. Writing scripts for RasMol, 2:45-3:15
   * * * Coffee/Juice Break! 3:15-3:30 * * *

9. Demonstration of MAGE, UCB-RasMol, 3:30-4:00

10. Downloading, installing, running a RasMol "movie" script, 4:00-4:30

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

1. Questionnaires, Intro to Participants and Workshop, 9:00-9:40

2. Netscape, RasMol Classic Main Page, 9:40-10:10

• Login to your computer using the number on your name tag (01-40).
• Run Netscape.
• Go to the RasMol Classic Main Page and explore it. www.umass.edu/microbio/rasmol
• Find the RasMol Manual (in web-readable html form) and Bookmark it.

• 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.
• Netscape is on the Apple Menu. If it weren't, you could use Finder.

• 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.
• Click the Start button at the lower left corner of your screen, and on the menu, open Programs, Network Applications (Server).
• Click on Netscape Navigator.

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

• Download and install RasMol.

• In Netscape, at the RasMol Classic Main Page, click on "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, but in this lab,they appear in the folder User's Folder. After the sit.hqx file is automatically unpacked, you can delete the sit.hqx (binhexed) file, and the sit (StuffIT compressed) file, leaving only the RasMac folder.
• Open the Macintosh HD icon (upper right of the desktop), and in that folder open User's Folder (and keep it open for the rest of the day). Close the Macintosh HD folder.
• In the User's Folder, open the RasMac folder. Drag the RasMac application out of its folder into the User's 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.
• Run RasMac. Use the File menu to Open 1d66.pdb (gal4 transcriptional regulator bound to DNA). The molecule should appear in the black window.

• In Netscape, at the RasMol Classic Main Page, click on "getting RasMol", then "getting and installing RasMol", then "RasWin for PC/Windows", then "32-bit RasWin". (We are using Windows NT 4 in the CRC. At home, pick the version which matches your computer.)
• The default path for saving files (drive D:) is not accessible for security reasons. Click the cancel icon, which gives you the Save As... dialog. Select My Computer and then Workshop##$ on 'Forbin' (J:), and then the folder named PDB.
• Open your PDB folder. Open (double-click) My Computer (an icon at the far upper left of the screen), and there open folder Workshop##$ on 'Forbin' (J:), and there open the PDB folder. In this folder you should see an icon of 3 gray balls, which is RasMol's icon (here named rw32b2a for RasWin 32-bit version 2.6 Beta 2a). 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.
• Open RasMol, and its black window should appear. Use RasMol's 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.

Important features to try out:

• Click to report atom/residue identification in command-line window.
  The report appears in RasMol's white command line window. Macs: it is behind the black window; move it. Windows: it starts minimized. Look at the Start menu bar (bottom of your screen), find RasMol Command Line and click to open it. Then move so you can see both the black and white windows.
• Display representations: wireframe, backbone, sticks, ball-and-stick, cartoons
• 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.)
• Options: Slab, specular, shadows, stereo, labels
• Export: GIF (to put images on web), color postscript to print hi-res (see Martz FAQ [Frequently Asked Questions] at the RasMol Classic Main Page, www.umass.edu/microbio/rasmol/faq_em.htm#printres ).

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

• Learn to use RasMol's command-line window.
• Follows 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, the command-line window starts minimized to an icon, and may be behind other windows. See http://www.umass.edu/microbio/rasmol/1st-run.txt.
• Web Manual (similar to Windows Help Menu), built-in help command (rasmol.hlp must be in same folder).
• Most important commands: 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

• Using the new "3DB Browser", search for a molecule of your choice, download the PDB file, and explore it in RasMol.

• In Netscape, go to www.pdb.bnl.gov. Bookmark it!
• Just below the second thick blue line, click Searching and browsing the PDB, then select 3DB Browser .
• Enter your search terms in the second slot, labeled Full text query of PDB data (not in PDB ID code).
• Press the button Start a search.
• Select a molecule in the list and press Retrieve data button.
• If you want more info before downloading the whole molecule (can be quite large), press Header only and read it. Then use the Back button of Netscape. If you don't want it, back up and pick another molecule.
• To get the whole molecule, press complete with coordinates, wait till Netscape says Document Done at the bottom, then File and Save as (into your PDB folder on J:). Before pressing the Save button, rename the file from the useless default name send-pdb to the unique 4-character Brookhaven ID code plus .pdb, e.g. 1d66.pdb.
• Open the file in RasMol and explore it!

• PDB = Protein Data Bank, also a common data file format for atomic coordinate files.
• Other sources of molecules including micromolecules are at Molecules Galore on the web site.
• If you have time, click on a blue/linked reference in a PDB file to jump to the National Center for Biotechnology Information's extremely useful WWW Entrez system. This integrates sequences, bibliographic references, and 3D structural information in a single user-friendly interface.

7. Chime, 2:15-2:45

• Chime is already installed on your computers -- go ahead and explore some Chime tutorials.
• Macintosh: Optionally practice downloading and installing Chime. There is one important trick to this (see Procedures below). Windows: Don't practice downloading and installing Chime because (i) it is totally automatic and easy, and (ii) it can't be done on your workshop computers for technical reasons.

• In Netscape, from the RasMol Classic Main Page, select "BioMolecules in the Classroom", then "Animated Tutorials", then "Chime Resources from UMass". (You can also click on either of the Chime links near the top of the main Classic Main Page, but these links may disappear in the future.)
• Explore each of the links under Ready-to-run Chime tutorials.
• Macintosh Installation (Optional): Installation of Chime 1.0 on the Macintosh is tricky at one point, whereas installation in Windows is totally automatic.
  • Get Chime from http://www.mdli.com/chemscape/chime.
  • Now Quit from Netscape. Discard the hqx file after the Installer is unpacked to your desktop (or to User's Folder in the workshop). Run the Installer. When it asks you to Select Folder, you must specify the correct folder!
  • Use Finder to find the folder containing your Netscape application. This folder should contain a folder named plug-ins. Display its location (Apple-I for Info, note "Where: ...").
  • In Chime's Select Folder dialog, you want the Netscape Navigator folder at the top, with plug-ins highlighted in the list, then push the Select button. The Installation Location should now show "in the folder 'plug-ins'". Only when this is the case, click the Install button. (Unfortunately, Chime's installer will announce success regardless of whether you put Chime in the correct folder. If put in the wrong folder, Chime simply won't work.)
  • Restart Netscape, and use the pulldown menu Help, About Plug-ins. If Chemscape Chime is not listed, then it was installed in the wrong folder. That would mean you have several copies or versions of Netscape in various places. Figure out which is the active one and rerun the Chime Installer.

• Chime is available via links from the RasMol Classic Main Page, which take you to MDL Information Systems, Inc. at www.mdli.com/chemscape/chime     Chime is free to all users. Its principal architect is Tim Maffett at MDLI, who incorporated a number of features which facilitate development of educational tutorials.
• Back at home, if you have installed RasMol as a Netscape helper application (http://www.umass.edu/microbio/rasmol/cfgnsras.htm) Chime will supercede it. If you wish to disable Chime temporarily so that RasMol again serves as Netscape's molecule viewer, see http://www.umass.edu/microbio/rasmol/dischime.htm

8. Writing scripts for RasMol, 2:45-3:15

• 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 the folder containing 1d66.pdb (and on Macs, the RasMol application).

    select a
    color blue
    select t
    color yellow
    select g
    color green
    select c
    color red
    
    select (dna and backbone)
    color white
    background white
    
    echo
    echo DNA: Green, Carmine, Azure, Tweety-bird
    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 in any view of any molecule(s).

  • This scheme uses the following mnemonics for the 4 bases:

    G = Green

    C = Carmine (red)

    A = Azure (blue)

    T = Tweety bird (yellow)

    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 when run.
  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. A RasMol "movie" script is made by the latter process; a 10-minute one contains about 1,200 commands.

• 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, 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 Classic Main Page or the workshop handout Pedagogy of Molecular Visualization (also at www.umass.edu/microbio/rasmol/pedagogy.htm ) for more information on script-writing.

9. Demonstration of MAGE, UCB-RasMol, 3:30-4:00

• Consider the pros and cons of RasMol vs. MAGE and Berkeley-enhanced UCB-RasMol.

• All programs mentioned here are free.
• For more information about any of these or other similar programs, and to download the programs themselves, at the RasMol Classic Main Page, select Other Free Molecular Visualization Software, then Free Software, then MAGE, or UCB-RasMol, etc.

• MAGE by David Richardson and Robert M. Weill, Duke U.
  • MAGE runs on Windows, Macs, unix.
  • MAGE (unlike RasMol) is especially effective for comparing multiple configurations of a molecule.
  • MAGE is designed to show preset views which the author of the 'kinemage' (kinetic image script) wishes to show you, and has a series of pushbuttons for this purpose. Therefore MAGE doesn't lend itself to free-roaming exploration as well as does RasMol.
  • MAGE's images are mostly wireframe, not as pretty as RasMol's.
  • Has a separate, scrollable window for text, so can provide long accompanying texts. However, this facility is not as good as Chime, which can be accompanied by hypertext containing buttons that change the view.
  • Kinemages (MAGE scripts, "KINEtic iMAGEs"), which require some programming to prepare, are needed in order for MAGE to show a molecule. MAGE cannot load a PDB file directly.
  • Hundreds of kinemages are available on basic protein structure as well as many on more specialized topics. Many of these were written by Jane Richardson, or with her guidance. Kinemages accompany many articles in the journal Protein Science.

• UCB-RasMol by Marco Molinaro, U Cal Berkeley.
  • Runs on Windows, Macs, unix.
  • Allows up to 5 molecules to be loaded simultaneously and moved independently, hence docking. RasMol can only load one at a time.
  • Has some serious bugs.

• Other free visualization software especially worth a look includes Swiss PDB-Viewer, WebLab, and Cn3D.

10. Downloading, installing, running a RasMol "movie" script, 4:00-4:30

• Select a script, download it, run it.

• At the RasMol Classic Main Page, select "... Classroom", then "Animated Tutorials", then "RasMol 'movie' scripts". Please select one of these three to play in the workshop: DNA3P (DNA structure), HB1P (hemoglobin), AB2P (antibody).
• Macs:
  • Click on the .sea.hqx file for the script you want.
  • After the automatic unstuffing is completed, drag the sea.hqx, sea.hqx.1, and sea files (but not the "script.sea folder") into the trash.
  • Drag the RasMac application icon into/onto the new script folder.
  • Open the script folder, run RasMac, starting the script with command script filename. The filenames for these scripts are respectively dna3.top, hemoglob.top, antibody.top.
• Windows:
  • Click on the .exe file for the script you want. This will open the "Save as ..." dialog window. Before saving the file, we're going to give it its own folder (because it will unpack into dozens of files). First, select the PDB folder. Now, at the top of the window are two folder icons. If you point to either, an explanation appears. Create a new folder by clicking on the right icon. Give that folder a name and and double click on it. Pressing the "Save" button will then deposit the .exe file into your new folder.
  • Open the new folder by double clicking on it. (If you can't find it, open the "My computer" icon at the upper left of the screen, then the J: folder, then the PDB folder, then your new folder.)
  • Double click on the .exe file you just downloaded. This will decompress it into the many files which make up a "movie" script.
  • Find the RasWin program icon (probably in the PDB folder in the J: folder) and drag it into the new script folder.
  • Run RasWin and start the script with the command script filename. The filenames for these scripts are respectively dna3.top, hemoglob.top, antibody.top.
• A script can be killed, only while standing at a pause, with Control-D.

• Aren't Chime tutorials easier to run?! Most RasMol "movie" scripts are in the process of being ported to Chime.
• Detailed instructions, should you need them later at home, are in a file in the script folder named 00sptdoc.htm. Use Netscape's File, Open File, to view this document.

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

Checkout

• Be sure to take with you the Assignment document for Interval One.
• Please fill out an assessment form for today's workshop.
• Macintosh: The contents of your User's Folder will be erased! Put anything you want to keep (such as scripts, PDB files) on a diskette. If it is too large for a diskette, and you want it to be here for the next workshop, copy it to your workshop## folder. Open this folder by starting with the CRC Shared icon at the upper right of your desktop. It contains users, which contains home, which contains workshop, which contains folders for each workshop##, where ## is 01-40. We shall try to avoid erasing the contents of your workshop## folder until after the second workshop meeting but this is not guaranteed! Files too large for a diskette which you wish to use at home can be re-downloaded at home.

• Windows: We shall try to preserve the contents of your J: drive and PDB folder on J: through the second workshop meeting but this is not guaranteed! Anything which you wish to keep (such as scripts you have written) should be copied to a diskette to take home. Files too large for a diskette can be re-downloaded at home.