Day 1: Installation and use of RasMol to visualize molecules
of your choice.
Workshop on Molecular Visualization for Biological Science Teaching:
RasMol and Chime
(U Mass, Amherst MA)
Long Island University, Brooklyn, Library Learning Center Room LLC 234B.
Assisted by Rashie Athukorala, Tim Driscoll, and Andrew Wing Lam.
LIU Liason, Professor Anthony dePass.
Computer facility preparation by Delicia Garnes and Darina Hasprunar.
Supported by the Undergraduate Faculty Enhancement Program of the
Division of Undergraduate Education, NSF, LIU 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/w1agend2.htm
Overview of Three Meetings and Two Intervals
Interval One: (3-6 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.
Overview of Day One
- Netscape, RasMol Web Site, 9:00-9:30
- Questionnaires, Intro to Participants and Workshop 9:30-10:10
- Downloading and Installing RasMol, 10:10-10:30
* * * Coffee Break, 10:30-10:50 * * *
- Basic RasMol: mouse, pull-down menus, 10:50-11:20
- RasMol Commands, 11:20-12:00
* * * Lunch! (For Goodness Steak) 12:00-1:30 * * *
- Downloading molecules of your choice from Brookhaven's
- Writing scripts for RasMol, 2:15-3:10
* * * Coffee/Juice Break! 3:10-3:30 * * *
- Chime, 3:30-4:00
- Demonstration of MAGE, Swiss-PDB-Viewer 4:00-4:30
- Assignments for Interval 1, Discussion, Evaluation 4:30-5:00
1. Netscape, RasMol Web Site, 9:00-9:30
- Run Netscape Navigator.
- Go to the RasMol Web Site and explore it.
- Find the RasMol Manual and Bookmark it.
- Save your bookmarks to a disk.
- Disable file extension hiding (applies to Windows only).
Explore the RasMol Web Site
- Run Netscape Navigator.
- Go to the RasMol Web Site and explore it. www.umass.edu/microbio/rasmol
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
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.
- Click on the Bookmarks pull-down menu of Netscape.
- Click on Go to 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. When Netscape is loaded up again, it will go to the disk drive to
search for and retrieve your bookmark file. However, if your disk is not in
the drive at the time that you reload Netscape, it will use its default blank bookmark
file for this and all subsequent sessions. At this point you can reload your bookmark
file by following the above-mentioned procedure except instead of saving a file in
File pull-down menu of the Booksmarks window, Open your file from
3.5 Floppy (A:).
Disabling Windows file-extension hiding
- If you use Windows 95 at home, you should do this on your computer
at home, too!
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 causes problems when
instructing RasMol which files you want it to use.
2. Questionnaires, Intro to Participants and Workshop, 9:30-10:10
- Fill out workshop questionnaires, 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 in a
folder named Friday or Saturday (according to what day
it is). 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 C:,
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 95 in
the LIU lab. At home, pick the version which matches your
- 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
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
- Your system may be configured to unpack the .sit.hqx (binhexed)
file automatically, producing an .sit (StuffIT compressed)
file, and then a "RasMol 2.6" folder. If not, 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
- You can delete the sit.hqx file, and the .sit file, leaving only
the "RasMol 2.6" folder.
- Create a working folder in which to put the RasMac application,
PDB files to view with it, scripts, etc. You can name this whatever
you wish (e.g. RasMac Working Folder), but we'll refer to it
throughout the remainder of this document as your Working Folder.
- Now you need some PDB files. A good bunch to start with can be
downloaded from RasMol Quick Start at
these in your Working Folder. We'll assume 1d66.pdb is there.
- 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
- Run RasMac. Use the File menu to Open 1d66.pdb (gal4
transcriptional regulator bound to DNA).
The molecule should appear in the black window.
Coffee Break! 10:30-10:50
4. Basic RasMol: mouse, pull-down menus, 10:50-11:20
- Learn to use the mouse.
- Try out the most important menu options.
These mouse click-and-drag operations work in RasMol and similarly (but with
some different details) in Chime.
|Mouse Click and Drag Summary
*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
- Try these from the Options menu: Slab, specular, shadows,
- 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
5. RasMol Commands, 11:20-12:00
- 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!
- The most important commands/terms are: selection vs. restriction; hetero
atoms; predefined groups of residues (e.g. hydrophobic); labeling;
hbonds and ssbonds; within.
Lunch! (For Goodness Steak) 12:00-1:30
6. Downloading molecules of your choice from Brookhaven's PDB, 1:30-2:15
- 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.
- Follow the numbered instructions on that page, saving the file
to your Working Directory.
- Open the file in RasMol and explore it!
- PDB = Protein Data Bank, also a common data file format for atomic
coordinate files. Each PDB atomic coordinate data file has an arbitrary
four character identifier (digits and letters), such as
1d66, 1hho, 1hbs, 2hhd, 1lfa, 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
7. Writing scripts for RasMol, 2:15-3:10
- 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
- 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:
- 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
select (dna and backbone)
echo DNA: Green, Carmine, Azure, Tweety-bird
- 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:
rotate z 90
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.
- RasMol-saved scripts created automatically
using a save script filename command. These generate
a single view when run.
- 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
- RasMol scripts have serious limitations. RasMol
scripts: 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
) for more information on script-writing.
Coffee/Juice/Cookie Break! 3:10-3:30
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.
Macintosh Installation at home: Installation of
Chime 1.0 on the Macintosh is tricky at one point, whereas
installation in Windows is totally automatic.
- View some Chime presentations.
In Netscape, from the RasMol Web Site, select Chime.
Explore some of the Ready-to-run Chime
- Practice downloading and installing Chime. In Netscape,
go to the source of Chime, MDL Information Systems Inc., www.mdli.com. Click on the
Chemscape Now! button in the left column, then click on
Chemscape Chime. Select Download Chime 1.0, the Win95
version, and save the Chime installer file to the Desktop.
Chime 2 requires Navigator 4.x which is not available in the LIU computer
At home, if you have Navigator 4.x installed, you may try out Chime 2.
It has many amazing new features, including an extensive menu for selecting
atoms, residues, chains, and predefined sets.
Get Chime from
Now Quit from Netscape. Discard the .hqx file after the Installer is
unpacked to your desktop. Run the Installer. When it asks you to
Select Folder, you must specify the correct folder!
In the Finder, use the File menu's Find option
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 Web Site, which take
you to MDL Information Systems, Inc. at www.mdli.com/chemscape/chime
Chime is free to all users. Its
principal architects are Tim Maffett and Bryan van Vliet at MDLI, who
kindly incorporated a number of suggestions which facilitate development of
9. Demonstration of MAGE, Swiss-PDB-Viewer, 4:00-4:30
Understand the unique strengths of MAGE and Swiss-PDB-Viewer.
- 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 Web Site,
select Index, then Other Free Molecular Visualization
Tools, Galleries, and Resources, then Free Software.
- 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
- 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.
- Swiss PDB Viewer by Nicolas Guex, GlaxoWellcome.
- Steeper learning curve, but has powerful modeling capabilities
lacking in the visualizers RasMol, Chime, or MAGE. An excellent introductory
tutorial by Gale Rhodes is available.
- Can load and manipulate multiple molecules. Can align similar
molecules and color residues by distances between them. Can perform
symmetry and matrix operations (for example, make a hemoglobin
tetramer from a PDB file which has only half of the tetramer).
- Can 'mutate' an amino acid, and find best angle for side chain (rotamer
analysis). Can change Phi and Psi angles for individual
amino acids by dragging the point on the Ramachandran plot.
- Determines hydrogen bonds according to distances of acceptors and donors.
- Can rapidly switch between alternate configurations (similar to MAGE).
- Limitations: Representations are limited to wireframe, strands, and dot
surfaces. H-bonds, labels, and dot surfaces disappear when rotating. (Stereo is
well implemented.) No mechanism for pre-programmed tutorials or hypertext.
10. Assignments for Interval 1, Evaluation, Discussion, 4:30-5:00
- Be sure to take with you the Assignment and Pedagogy
documents for Interval One.
- Please fill out an assessment form for today's workshop.
- Anything which you wish to keep (such as scripts you have written,
PDB files you downloaded, and bookmarks you have saved) should be
saved to a diskette to take home. Files too large for a diskette can
be re-downloaded at home.
Thanks to Rashie Athukorala and Tim Driscoll
for assistance with parts of this document.