RasTop 1.3.1

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 1.3.1
by Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA,
valadon@ix.netcom.com
Versions 1.3, August 2000 and 1.3.1, March 2001
Copyright © Philippe Valadon 2000

INTRODUCTION

Our understanding in biological sciences is progressing rapidly. More and more proteins are discovered everyday, new ways on how they associate in superstructures are elucidated. RasTop was developed with the idea of giving to the scientist, "at the bench", a mean to visualize quickly the tri-dimensional shape of macromolecules.

RasTop is a graphical interface to the program RasMol adapted for Windows platform. RasTop wraps 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 many extensions to handle atom selections: addition and subtraction of atoms, selection with a lasso, copying to and pasting from the clipboard, and a full saving of a work session under a script format called RSM script. RasTop allows several molecules to be opened at the same time (on different windows) and provides a limited editing of the molecular file.

We would like to thank Roger Sayle, Anne Muller and Herbert J. Bernstein for giving RasMol freely to the community, and all the people who contributed directly or indirectly to RasMol by their reports, correction, or 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 Bernstein, Frances Bernstein, William McClure, Eric Marz, Margaret Wong, and Roger Sayle for their contributions to the Help file and giving the permission to re-use their work.

Special thanks to Herbert Bernstein for creating the OpenRasmol site and promoting the distribution of RasTop.

COMPATIBILITY

RasTop 1.3.1 is available for Windows 95, 98, NT, and 2000 platforms. The present version has not been fully tested on Windows ME, but no major problem have been reported so far.

Recommended hardware:  A Pentium or equivalent processor is recommended, as well as 16 MB of RAM. A web browser is required to access the help site, at best a version 4 or higher, but no connection to the network (local, www, internet, etc.) is required. Many web browsers are available free of charge.

NOTICE

RasTop is an open project with an open source; everybody is welcome to contribute to its development, but, as a derivative of the program RasMol 2.7.1, certain restrictions apply to it. Please, read carefully the full notice located in the help folder.

RasTop Notice:

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

2. RASTOP 1.3.1 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 1.3.1 standard package, including binary, complete source code, and user documentation may be obtained by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/RasTop_1.3.1/RasTop.zip

or on the web at:

The standard package contains RasTop 1.3.1 32-bits version. If your monitor only supports 256 colors, consult the Custom Installation paragraph.

Standard Installation: 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 on Windows 9x platforms, proceed as following:

• 1) Right-click on RasTop.exe file 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. If you get a message saying: "The RASTOP.EXE file is linked to missing MFC42.DLL:6605" and RasTop does not start, consult the paragraph Custom Installation.

Click under the file>Preferences menu option to activate the Preferences dialog box. Set the size of the control panel if necessary. Locate the help folder in the RasTop folder by browsing the hard-drive and selecting the file "default.html".

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.

Custom Installation:

If your monitor only supports 256 colors, download the rastop_8bit.zip file by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/RasTop_1.3.1/RasTop_8bit.zip

or on the web at:

http://www.bernstein-plus-sons.com/software/RasTop_1.3.1/RasTop_8bit.zip

Unzip and replace the original, 32 bit, exe file - RasTop.exe -  by the new exe file. Change the name back to RasTop.exe if you wish.

If you cannot get started and always receive the warning message "The RASTOP.EXE file is linked to missing MFC42.DLL:6605", download the missing dll at:

ftp://ftp.bernstein-plus-sons.com/software/RasTop_1.3.1/mfc42.zip

or on the web at:

http://www.bernstein-plus-sons.com/software/RasTop_1.3.1/mfc42.zip

Unzip the patch and  install the file mfc42.dll in the folder containing the RasTop.exe file.

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 1.3.1 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 large molecules were opened.

Save your work regularly. If you make drastic changes, save on a different name.

RasTop 1.3.1 - This release
This is a minor update with modifications concerning mainly correction of bugs reported for the 1.3 version. The software is now supported under Windows 2000 operating system. The software seems also stable under Windows ME. A release for 8-bit monitors is also available (although never tested on a true 256 colors monitor). A few systems are missing an updated version of the mfc42.dll file which is also available, but requires separate installation.

Limitation of the present version (read me)

The routines to export picture files are still under their initial 8-bit version and therefore do not work in the 32-bit version. The PICT format seems to work. The clipboard is the best way to export pictures.

Rendering improvements such as depth plane are not included in the export formats POVRay and MolScript. This could result in some severe limitations since it blocks the transfer of certain pieces of work outside from RasTop.

The shadow mode does not work properly and often causes severe crashes.

RasTop 1.3 - Released August 2000
This is the first release of RasTop. Beside the interface, new rendering capabilities were added to RasMol code: back clipping, 32-bit output under Windows, centering command either on current selection or to the origin, variation of depthcue in slab mode, and ShadePower coloring feature.

COMMENTS AND SUGGESTIONS

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

As part of RasMol project, comments and suggestions on RasTop, especially those regarding RasMol, the open source license, or contributions to RasMol/RasTop, are also welcome by Herbert Bernstein at rasmol@bernstein-plus-sons.com.

Updated
by Philippe Valadon
with minor changes 15 April 2001
by Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
+1-631-286-1339