RasTop 1.3

Based on RasMol 2.6 by Roger Sayle
Biomolecular Structures Group, Glaxo Wellcome Research & Development
Stevenage, Hertfordshire, UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright © Roger Sayle 1992-1999

And based on Mods by Arne Mueller
Version 2.6x1, May 1998
Copyright © Arne Mueller 1998

And based on RasMol 2.7.1 by Herbert J. Bernstein
Bernstein + Sons, P.O. Box 177, Bellport, NY, USA, yaya@bernstein-plus-sons.com
2.7.0 March 1999, 2.7.1 June 1999
Copyright © Herbert J. Bernstein 1998-1999

RasTop 1.3
by Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA,
valadon@ix.netcom.com
Version 1.3, August 2000
Copyright © Philippe Valadon 2000

INTRODUCTION

RasTop is a graphical interface to the program RasMol. RasMol is a molecular graphics program developed initially by Roger Sayle and intended for the visualization of proteins, nucleic acids and small molecules. RasTop offers a user-friendly graphical interface around "RasMol molecular engine". No more typing on the command line, each command in the menu generates its own script that is transferred to RasMol. RasTop has numerous extensions to handle atom selections: addition and subtraction of atoms, groups, or chains, selection on screen with a lasso, ability to go back to the previous selection, copying to and pasting selections from the clipboard, new set operations such as inverse, extraction, summation, subtraction, and exclusion, and finally full saving of all user-defined atom sets under an extended script format called RSM script.

Along its development, a few new capabilities were added to the "classical" RasMol program: back clipping, 32-bit output under Windows, full centering command either on a selected atom or to the origin, variation of depthcue in slab mode, and a coloring command, shadepower, which generates new metal-like surfaces.

RasTop allows several molecules to be opened at the same time (on different windows) and provides a limited editing of the molecular file.

OBJECTIVE

RasTop was at first a programming experience, but rapidly became a project on its own.  The use of scripting, a kind of markup language for molecular rendering, makes RasMol an outstanding teaching tool. On the other hand, the command line is rather a lengthy process and saving a work session is not particularly easy. This is where holds RasTop main idea, a tool "for scientist," "at the bench," to handle rapidly a macromolecule in its three-dimensional representation.

We would like to thank Roger Sayle, Anne Muller and Herbert J. Berstein for giving RasMol freely to the community, not forgetting all the people who contributed by their bug reports and code improvements. It is a wonderful experience to enter RasMol project and we encourage all of you to continue the work. Many thanks also to Herbert Berstein, Frances Bernstein, William McClure, Eric Marz, Margaret Wong, and Roger Sayle for their contributions to the Help and giving the permission to re-use their work.

COMPATIBILITY

RasTop 1.3 is only available for Windows 95, 98 and NT platforms.

NOTICE

RasTop Notice:

1.  Before using RasTop, contributing to the source, or using any of its material, you must read and comply with all notices constituted of RasTop 1.3 Notice, RasMol 2.7.1 Notice, RasMolv2.6 Notice, IUCR Policy, CBFLIB Notice, and CIFPARSE Notice.

2. RASTOP 1.3 PROGRAMS AND DOCUMENTS AND ANY FILES CREATED BY THE PROGRAMS ARE PROVIDED **AS IS** WITHOUT WARRANTY OF ANY KIND. THE AUTHOR DISCLAIMS ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING THE WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DAMAGES WHATSOEVER. THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE, OR FILES AND NOT WITH THE AUTHOR OF THE PROGRAMS OR DOCUMENTS.

3.  THE RASMOL 2.7.1. NOTICE APPLIES TO RASTOP 1.3 AS A WHOLE.

4.  If you publish any work done with this package, you must give credit by citing this package, its authors, and an URL where to find the package or the source from which you obtained it. This requirement for citation includes any molecular graphics images created with RasTop and published in scientific journals.

5. If you do not agree with the terms and conditions stated in the full notice, please do not use RASTOP.

SOURCE CODE AND BINARIES

RasTop 1.3 full package, including binary, complete source code, and user documentation may be obtained by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/rastop/RasTop.zip

or on the web at:

http://www.bernstein-plus-sons.com/software/rastop/RasTop.zip

Installing RasTop: Extract the RasTop folder from the RasTop.zip file. Install the RasTop folder in the directory of your choice.

To get RasTop icon in the start-up manager, proceed as following:

1) Right-click on RasTop.exe and select 'create shortcut';
2) Transfer the shortcut into the folder  "C://Windows/Start Menu/Programs".

To start RasTop, double-click on the RasTop icon. When started for the first time, the program displays a single main window and one empty graphic window.

RasTop is a multi-document interface. Several graphic windows, each displaying a single molecular file, can be opened at the same time. Graphic windows are independent from each other, but can communicate using the clipboard to transfer various information such as spatial position or current atom selection. The same molecular file can be opened simultaneously in different graphic windows.

Setting the preferences:

1) Click under the file>Preferences menu option to activate the Preferences dialog box.

2) Fix the size of the control panel if it appears too small or too large on your screen.

3) Locate the help source. Browse your hard-drive and select the file "default.html" in the RasTop help folder.

Using the help: Open your browser off-line. No connection to the internet is required; any browser, preferably a version 4.0 or higher, is needed. Open any page (a file with the extension <*.html> in the RasTop help folder, and navigate or use the menu command help>help rastop in RasTop if the Preferences have been set.

CAUTIONS

*** THIS IS A PRELIMINARY RELEASE - USE WITH CAUTION ***

RasTop 1.3, like RasMol 2.7.1, contains a lot of new code. Under its current version, RasMol 1.3 has been extensively tested with molecular files in pdb format and showed good stability. Nevertheless you should be careful in testing other formats.

RasTop makes an extended use of memory, especially if you open several molecular files at the same time. Each time you close all opened molecule windows, the excess of memory occupied by RasTop is freed. Do this operation each time you terminate a session where big molecules were opened.

Save your work regularly.  If you make drastic changes, save on a different name. An unknown bug still causes the program to stop unpredictably.

The file opening mechanism is still fragile. Behavior on erroneous files or erroneous openings are not totally under control. Not all file types have been tested.

There is a probable bug with boundaries on some selection operations. Verify regularly your current selection in the mode "selection display."

During automatic rotation (automode), dialogs activated by the menu are often send behind RasTop window. Click anywhere in Windows, for example on the start button on the lower left corner of the screen, and click again on RasTop window to access the dialog.

Please, report bugs and uncontrolled behavior to the author.

COMMENTS AND SUGGESTIONS

Any comments, suggestions or questions about RasTop can be directed to its author at valadon@ix.netcom.com.