                            RASTOP

                MOLECULAR VISUALIZATION SOFTWARE

                    By Philippe Valadon
                Version 2.0.3, January 2003 
            Copyright (c) Philippe Valadon 2000-2003


INTRODUCTION

Welcome to RasTop molecular visualization software, Version 2.0.3.

RasTop is a molecular graphics program intended for the 
visualization of proteins, nucleic acids and small molecules. 
The program is aimed at display, teaching and generation of 
publication quality images. 

RasTop is derived from the software RasMol initially developed
by Roger Sayle. Different from RasMol, RasTop does not have
a command line to enter commands manually, but offers a 
user-friendly graphical interface. There is no more typing 
on the command line and each command in the menu generates 
its own script that is transferred internally to RasMol. 

The current release of RasTop is derived from RasMol version 
2.7.1 and RasTop version 1.3.1.  Along its development, many
new capabilities were added, in particular numerous ways to 
handle atom selections, an extended script format called RSM 
script to save and restore work sessions, and improvements of 
molecule rendering.

RasTop allows multiple molecules to be opened in one window 
and several windows to be active at the same time.


WHAT IS NEW IN RASTOP VERSION 2.0.3

The 2.0.3 version is a minor update over the 2.0 version.
RasTop now exports Povray scripts that can be rendered 
with high quality using the software povray, version 3.5.
Povray is available at www.povray.org.

Here are briefly listed the main modifications of the 2.0 
Version over the previous one:

Interface improvements: New toolbar with direct selection of 
atom properties and element sets; new buttons to facilitate 
rendering. The mouse wheel is now active. Information on 
pointed atoms available in the status bar. Hopefully the program 
is working without problem on Windows 2000 platforms.

Rendering improvements: Higher color resolution and depth queuing. 
New cylinder rendering, multidirectional headlight, better 
cartoon and ribbon rendering, more comprehensive display mode, 
Richards - Connolly surfaces, choice of molecular rendering
at start from a default script and preference saving.

Multiple molecule capability: Fully loaded world accepting 
multiple molecules; saving and restoring of complete worlds 
with improved world scripting.


WHAT DOES NOT WORK IN RASTOP

Always good to know before! The mode shadow does not work properly
and makes RasTop to crash frequently.  The export of graphic files
does not work for all formats in the 32-bit version.  The PICT 
format works ok, but the best way to export images is the 
clipboard. Rendering improvements and multiple molecules are not 
included in every script export formats (in version 2.0.3, only
povray export is working).


RECOMMENDED HARDWARE

RasTop makes an extended use of memory, especially if you 
open several molecular files at the same time. 

To run RasTop, 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 ON USING RASTOP, WORKING OR USING THE SOURCE, COPYRIGHT

RasTop 2.0.3 is open source, but is not in the public domain. 
Certain conditions apply to users and to developers to ensure 
that RasTop 2.0 and RasMol 2.7.2 from which it derived remain
open source. Read the full NOTICE located in the help folder.

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 Notice, RasMol 2.7.1. Notice, RasMolv2.6. 
Notice, IUCR Policy, CBFLIB Notice, and CIFPARSE Notice.

2.  RASTOP 2.0 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 WIH THE AUTHOR OF THE 
PROGRAMS OR DOCUMENTS.

3.  THE RASMOL 2.7.1. NOTICE APPLIES TO RASTOP 2.0 AS A WHOLE.
 
4.  If you do not agree with the terms and conditions stated in 
the full notice, please do not use RASTOP.


WHAT DO I NEED, 32-bit or 8-bit VERSION?

The vast majority of monitor now uses full color and therefore
the 32-bit version is your first choice.  If you have any doubt
on the ability of your monitor to display all colors, or if RasTop
generates extremely poor color renderings, check you monitor 
properties by right-clicking anywhere on the desktop.


INSTALLING RASTOP

RasTop is only available for Windows 9x, Windows NT, and Windows 
2000 platforms.

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

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 one or several molecular files, can be opened 
at the same time. Graphic windows are independent from each 
other, but communicate using the clipboard to transfer various 
information such as spatial position or current atom selection.


SETTING THE PREFERENCES

In RasTop 2.0.3, Preferences are in the file "rasmolprefs" located
in your user directory ("C:\Documents and settings\yourname"). Preferences are automatically generated the first time you launch RasTop.

To set-up the preferences:

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

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


USING THE HELP FILE

Open your browser off-line.  Open any page (a file with the 
extension <*.html> in the RasTop help folder, and navigate 
or click in the menu option help>rastop help in RasTop if the 
preferences have been set.


GETTING STARTED WITH MOLECULES

Read the tutorial in the help.


CONTRIBUTING TO RASTOP PROJECT

If you notice any bugs or strange behaviors, please contact the 
author. All code improvements are welcome.

------------------------------------------------------
Philippe Valadon
P.O. Box 13014, La Jolla, CA 928064, USA,
valadon@ix.netcom.com
Version 2.0.3, January 2003 
Copyright (c) Philippe Valadon 2000-2003

San Diego, January 20, 2002.
