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    Introductions to: RasMol v2.5     HTML & 2.6 Versions

RasMol Version 2.6-beta-2 Manual

Molecular Visualisation Program

Roger Sayle
Glaxo Wellcome Research and Development
Stevenage, Hertfordshire, U.K.

In May 1997, Dr. William McClure at Carnegie Mellon University divided rasman.htm into 22 files for faster navigation in a frames or linked page format. Except for the additions listed below, very little was changed in the content or format of the original hypertext version of the Manual, rasman.htm.
The following pages were added to this version:

1. A two-page PDF version of the "RasMol Quick Reference Card" was added as a link under Navigation Notes.
2. A page illustrating the Pull Down Menu selections was added to the section on RasMol's Window in General Operation.
3. A Summary Table of amino acid classes was added to the Predefined Sets section.
4. Three tables that display Predefined Colors, Amino/Shapely Colors, and CPK Colors were added as a links under Colors and Color Schemes.
5. A page on Files and File Formats from the v2.5 Manual and v2.6 update. A PDP file Example page with a glossary of terms is also linked to this page.
6. The Bibliography from the v2.5 Manual; links to some of these references were added to the text.

Copied from the Introduction to rasman.htm:

In July, 1996, this version of the RasMol Manual was updated from version 2.5 to version 2.6-beta-2 by Dr. Margaret Wong of the Chemistry Department, Swinburne University of Technology, Australia (marg@chem1.chem.swin.edu.au). Some further revisions were made by Eric Martz (emartz@microbio.umass.edu), who will be happy to receive suggestions for additional improvements. Subsequent revisions are detailed below.

RasMol in versions for several operating systems, installation instructions, and extensive supplementary resources are available at the RasMol Home Page. Included are Frequently Asked Questions (FAQ), tutorials on how to use RasMol, several documents on how to create "movie" scripts, and Roger Sayle's personal account of how RasMol came to be. RasMol's original distribution site is by ftp from the University of Edinburgh.

Use the Find mechanism of your web browser to search for topics of interest. This is possible because this version of the Manual is a single html file (rather than being broken into a separate file for each chapter, as are some versions of the Manual you will find on the web). The disadvantage of this is that it may take some time to load the entire Manual (>140 kilobytes) into your browser. If you click on a topic which appears to be missing, just wait until the entire document has loaded ("Document: Done" message at the bottom of Netscape). If you will be referring to the Manual frequently, it is recommended that you use your web browser's File, Save to make a copy of the Manual on your local disk. You can then use your browser's local mode (File, Open) to view this file, which will load much more quickly. As long as you have installed your web browser on a computer, it does not need an Internet connection to view a local file.

Revision History

• 97/03/16: Expanded the section on the group color scheme, explaining the use of set hetero off to control the spectrum of colors. Also corrected the colors given for the ends of proteins, which were inadvertently reversed in the manual.
• 96/09/02: Added new section on the trace command, and revised backbone accordingly. Added dashes option to backbone, strands, and wireframe commands. Added section for set bonds. Added more detail about use of pause including synonymy with wait. Added section on set bonds. Indexed the section on set write under set (it had inadvertantly been omitted). Fixed incorrectly formatted "disappearing" instances of "<filename>". Added new section on exit which is now distinct from quit (see comments in html source).
• 96/08/14: Filename changed from rasman26.htm to rasman.htm so links will remain version-independent. Minor typos and formatting changes. This "single-file" version can be used to search the entire manual for key words, topics, etc.
• 96/08/13: Updated Introduction and added General Operations sections, which were taken from the non-html manual bundled with version 2.5. These were revised to bring them into accord with version 2.6 beta-2 (see comments in html source).

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    Introductions to: RasMol v2.5     HTML & 2.6 Versions