Maintenance and additions to this RasMol Classic Site largely ceased in 1999, when
RasMol was superceded by
Protein Explorer
and MolviZ.Org.
See also
What's New at MolviZ.Org
-- this information is not listed below.
What's New at the RasMol Classic Site
Here's a list of additions/changes to this site since Feb. 10, 1996,
most recent first. For visiting and downloading rates at this site, see
Site Statistics. In 1999, this site was visited
by 6,000 people/week during the academic year, and 4,000 people/week
during the summer.
2008
08/07/12: This site, formerly titled the RasMol Home Page,
was renamed the RasMol Classic Site, in deference
to the current RasMol Home Page,
RasMol.Org.
Jmol-based resources were recommended as an alternative to RasMol, and
Chime-based resources were deprecated.
2000
00/08/28: In a major transition, emphasis of the
main page
on this site changed from RasMol to Protein Explorer.
00/08/10: An update was provided
for participants in the 1997-1999 NSF-funded Workshops on
Molecular Visualization in Biological Science Teaching.
00/07/29: The
PDB Lite page was updated to ensure that all mirrors linked here
keep their databases up with weekly updates of the Protein Data Bank,
and that all sites are working properly.
00/06/26: The section listing the van der Waals radii used
by Chime and RasMol for spacefilling and dots has been revised and expanded in the
FAQ. It now includes the "united atom"
radii previously disclosed only in the email list discussion (and still
not mentioned under 'spacefill' in the reference manual).
January-December 1999
99/08/20: The FAQ now includes
"
Where can I find out how to use the "select" command?
"
and
"
What are the values used by RasMol and Chime for van der Waals radii in the spacefill rendering?
"
99/08/17: I have provided a new document for the FAQ,
which addresses these questions:
99/07/28: Two websites of major importance have recently moved.
All resulting broken links to
ExPASy have been fixed, and the most important 26 links to
the former Brookhaven PDB have now been fixed to work with the
new PDB at RCSB. (There are still
about 20 rarely used links to BNL not yet fixed.)
99/06/29: Thanks to the efforts of Herbert Bernstein,
Roger Sayle, Arne Mueller, and others, RasMol lives! In April,
they released
RasMol 2.7 with several important new
capabilities. (It was announced on the RasMol
EMail List.)
99/03/26: The
which was provided June, 1998 was disabled due to circumstances
beyond our control from approximately November 1998 until today.
Thanks to the generosity of the
Research Collaboratory for Structural
Bioinformatcs at the San Diego Supercomputer
Center we have been able to reinstate the Guestbook as of today.
Thanks also to Srinivas Turaga who helped to make this possible.
99/03/13: Thanks to Eric Francoeur, I have corrected my
spelling of Koltun in every place I could find it. Koltun is
the K in CPK. In case you have a local copy of
cpk.gif found in the reference manual and elsewhere on this site,
you may wish to download the corrected
cpk.gif.
99/02/11: Can RasMol be distributed freely, on CD-ROMs, and
used freely even for commercial purposes? Roger Sayle's resounding
Yes!
has been included in
his section of the FAQ.
July-December 1998
98/12/07: Is RasMol year-2000 (Y2K) compliant? Roger Sayle's
definitive answer has been added to his section of the
FAQ.
98/08/10: A Venn diagram summarizing the predefined terms useful
for selection in RasMol and Chime was contributed by Kurt Giles. It
has been incorporated into the overview of
select commands and the reference manual.
98/06/22: At long last, a
Guestbook has been created! You can now add links to your favorite resources
to the RasMol Classic Main Page.
(The Guestbook was discontinued ca. 2000 because it was superceded by
molvisindex.org.)
The Guestbook is linked to the Index Page
and has several sections devoted to specific topics. These topical
sections are in turn linked to relevant pages at this site.
We regret that maintenance of this site
has overtaxed the resources which we have to devote to it, and scores
of suggested links have not been completed. Hopefully, this Guestbook
will help to alleviate this problem.
98/06/22: Under Other Software, links
have been added for Kurt Wüthrich's MolMol which, together with
Pov-Ray, produces beautiful publication-quality images.
98/06/22: Some Chime tutorials in German have been linked
to the Non-English Resources page.
98/06/07: There is a new search interface at the Brookhaven
Protein Data Bank called PDB Lite.
PDB Lite was designed by Eric Martz and
implemented by Jaime Prilusky at the invitation of the Director of the
Protein Data Bank, Joel Sussman. PDB Lite makes it easier for students
and educators to find, view, and download PDB files for
macromolecules. The original search interface, the 3DB Browser
created by Jaime Prilusky, remains available to provide
the power and flexibility needed
by crystallographers and protein structure specialists, but is rather
technical and complex for novices or occasional users.
PDB Lite is linked to our page for
Getting Molecules.
98/05/16: PDB files for thousands of pharmaceuticals are available
from the Akira Dobashi group's site at Tokyo University in Japan.
Links are under Micromolecules
and the World Index of Animated Tutorials in Chime;
each molecule is also shown in Chime with molecular dynamics animation!
January-April 1998
98/04/27: A new guide to Select Commands in
Chime and RasMol has been provided. It explains how to select or
restrict (hide) atoms, residues, chains, ligands, groups of residues
(such as hydrophobic or charged), and nearest neighbors. It is linked
to RasMol Tutorials, and to several other
places.
98/04/13: For our workshops, a quick
reference handout has been prepared listing the RasMol/Chime Color RGB Values in decimal and
hexadecimal. This is helpful when making an HTML color key for Chime's
colors.
98/04/02: What can you learn about
a protein/DNA molecule with RasMol? has been revised and expanded.
It now includes not only a section which specifically
examines the protein:DNA complex 1d66.pdb, but also a new generic section
designed to guide you through the exploration of any macromolecule of
your choice.
98/03/27: Shareware for retaining your RasMol window sizes
and positions is now described in the Martz
FAQ. (Previously, this information was available in the
1997 history of the email discussion.)
98/02/28: More detailed information about RasMol's slab
command has been added to the
RasMol Manual.
98/02/27: College faculty in the New York City area (USA): there
is less than a week remaining to register for the
workshops at LIU, Brooklyn. Only a handful
of slots remain open.
98/02/26: The starter package of molecules offered to beginners
has been made more exciting. The ATP now has double bonds, and in
addition to the traditional protein:DNA complex (1d66.pdb), oxygenated
human hemoglobin and a lipid bilayer containing a channel have been
added. Get these from RasMol Quick Start.
98/02/24: Further improvements have been made to the page Where does one get "molecules", including the
repair of the broken links, thanks to Aron Sacchetti.
98/01/01: Swiss-PDBViewer can save subsets of residues in an
existing PDB file, and optionally with rotation, translation, and center
specified by the user. Details kindly provided by Nicolas Guex are at
PDB Tools,
September-December 1997
97/12/26: Information has been compiled on the capabilities
of RasMol, Chime, and WebLab to save subsets of atoms and modify
existing PDB files. See PDB Tools,
also linked under the Martz FAQ and under
molecules.
97/11/16: Visiting statistics have been analyzed for the past
academic year. Nearly 2 million files were served to 90,000 people
from 90 countries! See Stats.
97/11/11: The image of heme at the top of our
Gallery has been provided in an alternate form with a white background
suitable for printing.
97/11/04: Dates have been set for the 1998 series of free, NSF-supported
workshops taught by Eric Martz in Amherst MA and New York City. These
enable college faculty to use molecular visualization in their teaching.
(Participants pay their own travel.)
97/10/26: The long awaited PAUSED version of the RasMol "movie"
script on lipid bilayers and gramicidin has finally been provided.
Get it from the
bilayer section of the Martz scripts page.
97/08/17: A new page on the history
of molecular visualization. Have you ever heard of Byron's Bender?
See pictures of these pre-computer visualizations.
97/08/06: A new Overview of molecular
visualization resources for teachers is available. This was
designed for a one-page flier to hand out at the International Union of
Biochemistry and Molecular Biology in San Francisco, August 24-29, and
at the Education Satellite Meeting the preceding weekend.
97/07/29: Provided a new first page with
an animated GIF to show rotation to those
who have never seen it, and have not installed RasMol nor Chime. A new
and better search interface has been
provided for searching this site. Thanks to Chris Finlayson for his
design and implementation of the new first page and search interface.
97/04/03:
RasMol "movie" scripts developed by Eric Martz on DNA, antibody, and MHC
have been translated into French (with content
enhanced in the process).
97/04/01: A list of frequently asked questions, with answers,
has been contributed by Roger Sayle. My apologies to Roger for
taking far too long to find the time to put this
very useful FAQ on the web site.
97/04/01: Babel, a web interface to Babel, MolView, and other links were
added to the page on free software other than
RasMol, which was also reorganized and better indexed. Now included
is an amazing web form which allows you to submit a PDB to RasMol and
get back a single image without ever running RasMol! See the
Molecule to Image Converter Engine.
97/04/01: The broken downloading link for
Win32SOle has been fixed.
January-March 1997
97/03/21: Free workshops for college
bioscience faculty in the northeastern USA announced today for summer, 1997.
97/03/06: An explicit link has been provided for those wishing
to use RasMol on VAX/VMS systems.
97/01/22: Curious about the C language source code for RasMol?
Don't have a unix account to unpack the tar.gz file? I finally
got around to putting the
unpacked files on our ftp server.
97/01/02: See the tutorial on protein secondary structure greatly
enhanced for Chime 1.0, with a linear presentation control structure adaptable
to other Chime scripts.
96/12/10: An improved version of the Chime command-line interface
will be found under Chime Resources.
96/12/9: WebLab is great new free
software which can show alpha helices as cylinders, add hydrogen atoms,
rotate residues around a bond, and delete unwanted atoms.
96/12/2: Additions to Chime Resources including further resources
on protein secondary structure, an example of using the javascript
ButtonCallback mechanism, and additional advantages of RasMol.
See What's new at the UMass Chime Resources
Site.
November
96/11/29: RasMol command-line tutorials on alpha helices and beta strands
in various proteins by Duane Sears et al. have been added to the list of
tutorials on how to use RasMol.
96/11/25: It was made possible to
download the new Chime resources
for local use (faster operation, operation without a network connection,
studying the methods used, or using as templates from which to build new
Chime resources).
96/11/20: Roger Sayle has kindly provided a new version of RasWin
for Windows computers without floating point hardware (e.g. 386SX). He
has also fixed some bugs in the 16- and 32-bit versions which require
floating point hardware. To these new
versions have been added installation instructions for Windows 95.
Also, the PDB downloading instructions have been
updated to reflect
Brookhaven's newer 3DB Browser pages, their application/x-rasmol
button, etc.
96/11/07: See the wonderful new capabilities of Chime 0.99! How to use Chime (in Chime), How to
create Chime web pages, and new tutorials on protein secondary
structure and DNA.
96/09/09: The free molecular visualization software list now includes
Cn3D. Take a look at this exciting new software!
Also take a look at the new Chime Medical Biochemistry
tutorials from the U Kansas. RasMol for
Acorn 32-bit RISC OS was updated
to 2.6 beta-2 in late August.
96/09/04: Roger Sayle, due to popular demand, provides RasMol
2.6 beta-2 with stereo in a 16-bit
version.
96/09/02: Corrected a number of omissions, errors, and formatting
problems in the HTML version of the
RasMol Manual.
96/08/05: Educational scripts on hemoglobin structure, and on DNA structure,
previously available only packaged for Windows or unpackaged by ftp, were
provided as sea.hqx files packaged for the Mac.
Also, these two scripts were provided with
improved instructions for
installation and operation including new details for the Mac. As scripts
are revised, all will gradually be provided with similar documentation in a
uniform format.
July
96/07/29: Thanks to Margaret Wong, there is now a hypertext version
of the RasMol Manual which is up
to date with version 2.6-beta-2.
96/07/10: Provided instructions on how to
search this site.
June
96/06/26: Added the Chemistry Department of Imperial College to the
Major Web Sites section of Other Resources,
and the Rzepa/Whitaker Hyperactive
Molecules site to Non-RasMol Galleries.
96/06/19: Some additional Macintosh and unix details provided
in the script files section of the
Guide to Script Creation, but many details are still missing.
96/06/19: Item below extended to include Netscape 3 and Macintosh.
96/06/13: Provided detailed instructions for
configuring Netscape to invoke RasMol automatically for PDB files,
and for disabling Chime's interference if desired (in Windows -- Mac details
need to be filled in).
96/05/16: Provided step-by-step instructions for downloading a PDB
file from Brookhaven with Netscape (select "Molecules Galore"
twice). Clarified that RasMol scripts will not run (yet) on UCB-RasMol
(select Classroom, then Movie Scripts, then Martz Scripts).
96/05/03: Added paper by Casher et al. on hyperactive
molecules and chemical MIME types to the bibliography page, including
a link to the html version.
96/05/01: Nixon, Leach & Rzepa's Chime script on the photosynthetic
reaction center ("classroom", "movie scripts").
April
96/04/30: A whole bunch of great resources by David Marcey,
Kenyon College, Gambier OH US have been linked: a generic RasMol tutorial
for novices under "classroom"; an illustrated selection of
PDB's under "molecules galore"; a Chime script/tutorial on
the beta subunit of E. coli DNA polymerase III under "classroom",
then "movie scripts"; and a group of molecular animations
under "other software".
96/04/30: Chemscape Chime, a derivative of RasMol, is linked
under "getting RasMol" and also under "other free
software". Get this!
96/04/18: RasMol 2.6 beta-2 is available. It has stereo! See
"Getting RasMol Itself".
96/04/12: New gallery image (Martz section) "Peptides from
two different viruses in the same MHC". Added lipid bilayers
and gramicidin membrane channel PDB files to the page on
"Exclusive molecules". Released revised version of
DNA3 script (with 2 bugs fixed).
96/04/11: Provided new script illustrating structure of lipid
bilayers and membrane channel gramicidin (click on classroom, scripts).
This "movie" script runs about 10 minutes and contains over 3,000
RasMol commands! The Scripts Page was improved in a number of ways. In
particular, there are now specific gallery links from each script, and
a new document is there entitled "How to avoid the most common
roadblock encountered by first-time RasMol script runners". Updated
visiting rate statistics page.
March
96/03/24: Added "guestbook" at end of main page
("Who are you? ...").
96/03/14: Berkeley-enhanced RasMol-2.6-ucb-beta is now available
for beta test under Windows/Mac/unix. It can load up to 5 separate
molecules and move them independently. Links have also been provided
to RasMol for NEXTSTEP and Acorn Archimedes RISC OS. (Look under:
Getting RasMol Itself -> Getting and installing RasMol.)
96/03/12: Under Other Resources: Major sites: Education section
of the Crystallography section of the World Wide Virtual Library.
Galleries: Indiana University Molecular
Structure Center (look for stereo of Sulfur-8).
96/03/11: Protein structure classes at U Connecticut, Classroom page.
96/03/11: New decorations added to links to François
Savary's 'Representation of Molecular Models' and 'Rendering
Techniques' under Other Resources, Galleries.
96/03/11: PDB page now has links to new BNL document and UCSF
atom numbering document. Look under 'Molecules Galore' for PDB.
96/03/07: Three items added to bibliography (thanks to Chris Hogue).
DNA2 script made available (slower version of DNA1 for faster computer
configurations).
96/03/04: Plain text made available for scripts added March 3.
96/03/03: Added new script on hemoglobin, expanded script on
antibody:antigen, and expanded script on DNA. DOS versions only;
Mac and plain text will follow soon.
96/03/02: Added cutaway views of lipid bilayers (Gallery or Molecules
Galore).
96/03/01: Added Roger Sayle's images to the Gallery. New GIF of
deoxy and oxy heme decorates main gallery page.
February
96/02/28: Created the RasMol Bibliography page (linked to the main page
near the top).
96/02/28: Added a summary of visiting statistics for this site (linked
to the main page, at the bottom).
96/02/13: Added images of lipid bilayers (Gallery or Molecules Galore).
96/02/10: Ferritin tutorial link on the Classroom page (at the bottom).
This page is maintained by emartz@microbio.umass.edu
