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RasTop 2.0 Help
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About RasTop
Version History
About RasMol
About this site
Contributors to RasTop Source:
Roger Sayle
RasMol, all versions up to 2.6.4 1992 - December 1998
Arne Mueller
Mods Version 2.6x1
May 1998
Herbert J. Bernstein
RasMol Version 2.7.0, 2.7.1 Mods
June 1999
Philippe Valadon
RasTop Version 2.0
January 2002
Contributors to RasTop Manual
Roger Sayle
Margaret Wong
Eric Martz
William McClure
Herbert J. Bernstein
Philippe Valadon
Contact the author
Open RasMol Site:
Open Rasmol


RasTop 2.0

Molecular Graphics Visualization Tool
Philippe Valadon, January 2002

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Welcome to RasTop molecular visualization software, Version 2.0. RasTop is a graphical interface to the program RasMol adapted for Windows platform. RasTop allows the viewing and the direct manipulation of macromolecules and small molecules on screen.

  Check improvements in version 2.0:

RasMol was developed initially by Roger Sayle. Many people since contributed to its code. In 1999, Herbert J. Berstein released a compilated version named Rasmol 2.7.1 of different source variants under a GPL-like license (see  NOTICE). Many thanks to these people for giving RasMol freely to the community. 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.

If you want to learn more on the genesis of RasMol and on the initial work made by Roger Sayle, first at the University of Edinburgh, and further at Glaxo Research and Development, check out the RasMol Home Page by Eric Martz or visit the library for more links on RasMol.

Everybody is welcome to use RasTop, but you must read and comply with the NOTICE, which contains important disclaimers and information on using, distributing, and contributing to this project.

If you have any question, suggestion, correction, or bug report, please contact the author

Before using RasTop, contributing to the source, or using any of its material, you must read and comply with the entire NOTICE constituted of the General Notice and the linked pages: RasMol Notice, IUCR Policy, CBFLIB Notice, and CIFPARSE Notice.

up.gif (892 bytes)About RasTop

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 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, 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, set operations such as inverse, extraction, summation, subtraction, and exclusion, 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 in the same window and several windows to be opened at the same time.

Recommanded Hardware: Pentium or equivalent processor, 16 MB of RAM, and a web browser to access this site, at best a version 4 or higher.

up.gif (892 bytes)RasTop 2.0 and previous versions

RasTop 2.0

This is a major update over previous versions. Next are listed the main modifications:

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. Richards - Connolly surfaces, new cylinder rendering, multidirectional headlight, better cartoon and ribbon rendering, more comprehensive display mode. Choice of the 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.

RasTop 2.0 contains a lot of new code. Please report any strange behaviors or bugs. Modifications made to the code of the previous releases are summarized in the ChangeLog directory.

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, directional light, or multiple molecules are not included in all export formats, including 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 of the software (did it ever work?).

RasTop 1.3.1- Released March 2001
This is a minor update with modifications concerning mainly correction of bugs reported for the 1.3 version.  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.

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.

up.gif (892 bytes)About RasMol

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

The program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files. If connectivity information is not contained in the file this is calculated automatically. The loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, space-filling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface representations. Atoms may also be labelled with arbitrary text strings. Alternate conformers and multiple NMR models may be specially coloured and identified in atom labels. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. The displayed molecule may be rotated, translated, zoomed and z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dial box. RasMol can read a prepared list of commands from a 'script' file (or via inter-process communication) to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image. Finally, the rendered image may be written out in a variety of formats including either raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.

RasMol has been developed by Roger Sayle at the University of Edinburgh's Biocomputing Research Unit and the BioMolecular Structure Department, Glaxo Research and Development, Greenford, U.K.

RasMol is an open project; everybody is welcome to contribute to its development.  Note that RasMol 2.7.1 is not an open source, meaning that some restrictions may apply to developers. 

Please, read the important Notice applying for RasMol.

up.gif (892 bytes)About this Site

RasTop 2.0 package contains a folder named "help." This folder contains a series of html documents plus varied files that together create a web-based document. To view the help site, open a web browser offline, click 'open' in the file menu command, browse your directory, and choose the file 'index.html'. You can also link RasTop directly to this site in the preferences.


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(c) CopyRight Philippe Valadon © 2000-2002
All publishing rights reserved. 
Last updated on Sunday, January 13, 2002