RasMol "Movie" Scripts are obsolete! With one exception, all the
movie scripts below have been ported to Chime.
The Chime versions are listed in the World Index
of BioMolecular Tutorials in Chime.
The "movie" scripts below on DNA, hemoglobin, antibody, MHC, and
lac repressor have all been ported to Chime and we urge you to use
the newer format.
Chime offers a much easier to use
and
more effective format for chemical structure presentations/tutorials.
The "movie" script on Lipid Bilayers and Membrane Channels is the only one which has not yet been ported to Chime (porting is planned). Several of the "movie" scripts below are avaliable in French. The French versions have not yet been ported to Chime. |
If you have written a script of interest to others, contact
emartz@microbio.umass.edu.
Your script can be linked to, or distributed from this site, provided
it meets certain requirements.
What is a "movie" script and how does it work?
RasMol scripts cannot be viewed directly in your web browser. A
script must first be downloaded to your computer. In order to run the
script, you must have
downloaded and installed RasMol version
2.6
(these scripts will not run on version 2.5, nor on UCB-RasMol!).
Once you have downloaded and unpacked the script files, you simply
type, for example, script dna3.top in RasMol's command window,
and press Enter.
Details on how to install and run each script for both Windows and
Macintosh/PPC are in an html file, 00sptdoc.htm, which is included
with each script.
If you are setting out to run a script for the first time, READ
How to avoid the most common roadblock encountered
by first-time RasMol script runners NOW!
Most scripts are available in two forms. One form has pauses
(press any key to continue) and is good for illustrating a class
lecture, or for downloading and self-paced study by students. The other
form has no pauses (unpaused), so runs continuously, unattended.
This form is good for projection at a meeting where people are moving
around, or for an audience where the main issue is RasMol's script capability,
rather than the scientific content of the script.
Each script is a group of plain text files containing RasMol
commands, plus the PDB files (also plain text) for the molecules
included in the script. The only script-specific commands are
refresh and pause; all the other commands in scripts are
ordinary RasMol commands. To understand how these scripts work,
download one and examine the contents of the script files, and see
the tutorials on script-creation.
Windows. These scripts are provided as self-unpacking DOS
EXEcutable files. See BELOW for links to individual scripts. To
install a script, download the EXE file, place it in an otherwise empty
DOS directory, and run it (to unpack it). It will create a large
number of files, including all needed PDB files and a documentation
file with the same name as the script. More detailed instructions are
in the
documentation file accompanying each script.
MacIntosh. Thanks to Tom Manderfield of Carnegie
Mellon University, Pittsburgh PA USA, some the scripts have been re-packaged
for MacIntosh users in the form of sea.hqx files. See
BELOW for links to individual scripts. Scripts which have not been
so-packaged can be gotten by ftp as unpackaged files (see below).
Operating instructions are included
in the
documentation file accompanying each script.
Unix, VMS? If you can't use either of the above packing
formats, you can ftp the unpackaged script files (see below). In
the present versions, some load commands inadvertantly use upper case
filenames; unix users will have to change these to lower case (fgrep
for load in *.scr). This will be fixed as each script is updated (thanks to
Christoph Weber).
Getting unpackaged script files. Typically, dozens of files make
up the package for a 'single script'. Use anonymous ftp to
marlin.bio.umass.edu in
/pub/shareware/rasmol/scripts
in ASCII mode (all files making up a script are plain text,
either scripts themselves or PDB files). Pick the directory whose name
signifies the script you want and get ALL files in that directory. In
"old-fashioned" ftp, type "prompt" to toggle off a
query for each file, then "mget *" to multiple-get all the
files in the directory.
All scripts below require
RasMol version 2.6
(They will NOT run on version 2.5, nor on UCB-RasMol)
Scripts are available on the following topics:
See stills from this script in the gallery.
DNA3P (by E. Martz, released 96/03/03; revised 96/04/12,
96/08/04). An expanded version of DNA1/2 with many
pauses, designed for use in a lecture on DNA structure. Adds
views of adenine base, adenosine, AMP, ADP, and ATP. Shows DNA
replication, and a single-base mutation. Revised April 1996 to
fix CG hydrogen bonds and dATP, August 1996 to fix problems running
under RasMac.
Windows: The script is packed into the file DNA3P.EXE.
Mac: get dna3p.sea.hqx.
DNA2 (by E. Martz, released 3/7/96). Same as DNA1, but designed for
faster computers (e.g. RasWin32 on a 486DX/66 or better). If DNA1 goes
by too fast (less than 4 minutes) on your computer, try DNA2.
Windows: The script is packed into the file DNA2ZIP.EXE. One of the files included
is the documentation file DNA2.TXT.
Mac: An sea.hqx file will be linked here as soon as it
is available.
Meanwhile, you can get the script files by ftp (see instructions for
unpackaged files above).
DNA1 (by E. Martz, released 11/95): Runs unattended for about 5 minutes.
This version designed for slower computers (cf. DNA2 below). Designed
to introduce the power and glory of RasMol to a general audience of
biologists. Illustrates basic DNA structure. Shows several
representations of double helix backbone with and without bases, base
pairing including hydrogen bonding, the code (as color), and briefly
the yeast transcriptional activator Gal4 protein bound to the DNA.
Windows: The script is packed into the file DNA1ZIP.EXE. One of the files included
is the documentation file DNA1.TXT.
Mac: Get DNA1.sea.hqx.
Meanwhile, you can get the script files by ftp (see instructions for
unpackaged files above).
See still from this script at the top of the gallery.
HB1P (by E. Martz, released 96/3/3. Minor bug fixed 97/2/7.)
Many pauses, designed for lecture use or student exploration.
Introduces RasMol representations of protein structure briefly,
starting with glycine, then polymerization of amino acids to show a
peptide, then the backbone simplification. Shows the hemoglobin
tetramer with hemes, then details of the iron-heme complex, and
oxygenation thereof. Shows the two histidines which anchor the iron in
the protein, and the hydrophobic pocket in which the heme sits. Shows
the predominance of alpha helices; cuts out and zooms in on a single
alpha helix, showing the hydrogen bonding, and the hydrophobic vs.
hydrophilic sides of the helix. Slices (slab mode) the molecule, using
colors to distinguish hydrophobic, polar, and charged amino acids,
showing the predominance of the latter on the surface of the beta-chain
(with water), and of hydrophobic residues in the center. Ends with
sickle hemoglobin, showing the mutant valine-6 causing polymerization.
Windows: The script is packed into the file HB1P.EXE.
Mac: Get hb1p.sea.hqx.
See stills from this script in the gallery.
AB2P (by E. Martz, 3/3/96: This expanded version supercedes AB1). Many pauses; for
lecture or student use.
Introduces RasMol representations of
protein structure briefly, starting with glycine, then polymerization
of amino acids to show a peptide, then the backbone simplification, and
how disulfide bonds are represented in a backbone representation. Then
moves to a whole IgG1, shows the carbohydrate in the Fc, then
F(ab')2 showing heavy and light chains, disulfide bonds, exploring a
single Ig domain structure, the Fv, highlighting the 6 complementarity
determining regions (CDR's), the contact residues for lysozyme as they
relate to the CDR's, and the lysozyme epitope itself.
Windows: The script is packed into the file AB2ZIP.EXE. One of the files included
is the documentation file AB2.TXT.
Mac: An sea.hqx file will be linked here as soon as it
is available. Meanwhile, the old version is available as
antibody.sea.hqx.
See above for other downloading options via ftp.
MHC1 (by E. Martz, repaired 12/13/95): Illustrates basic structure of class I
Major Histocompatibility Complex protein, including the binding of the
peptide into the groove. Shows CD8-binding site, contact atoms
between beta-2 microglobulin and the alpha chain, how peptide
side-chains interact with the groove or "stick up" forming the
determinant recognized by the T cell, the differences in what the T
cell "sees" for Sendai virus vs. VSV peptide determinants, hydrogen
bonding of the ends and anchor residues of the peptide for MHC class I,
and MHC class II with the ends of the peptide sticking out of the
groove. Frequent pauses; for lecture or student use.
Windows: The script is packed into the file MHC1ZIP.EXE. One of the files included
is the documentation file MHC1.TXT.
Mac: Get mhc1.sea.hqx.
These files are also available by ftp from marlin.bio.umass.edu in
/pub/shareware/rasmol/distrib.
BILAYER1 (by E. Martz, released 4/11/96): This script begins with cholesterol
and phosphatidyl choline (PC), then assembles a model crystalline 200
PC bilayer (100 per leaflet) plus several thousand water molecules.
Results are shown for molecular dynamics simulations which yielded
gel-like and fluid-like configurations. Gramicidin is shown
imbedded in a slice of a lipid bilayer, with water molecules penetrating
the channel.
This script runs continuously
without pauses; a paused version is available below.
Windows: The script is packed into the file BIL1ZIP.EXE. One of the files included
is the documentation file BILAYER1.TXT.
Mac: An sea.hqx file will be linked here as soon as it
is available.
Meanwhile, you can get the script files by ftp (see instructions for
unpackaged files above).
BILAYR1P (by E. Martz and R. Athukorala, released 10/26/97):
PAUSED version with same content as BILAYER1.
Windows: The script is packed into the file BILAYR1P.EXE (1 megabyte; 4.5 megabytes
unzipped). After you download
and unzip this file, open the file 00sptdoc.htm in your web browser
for complete installation and operation instructions.
Mac: Please download
BILAYR1P.EXE and try unzipping it.
Let
me
know whether this works. (Our ftp server is out of room. The unzipped
files are 4.5 megabytes due to the large PDB files included.)
Images from these scripts can be seen in the
RasMol Gallery.
This page is maintained by emartz@microbio.umass.edu