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RasTop 1.3. Help
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Content:
About RasTop
About RasMol
About this site
Contributors to RasTop Source:
Roger Sayle
RasMol, all versions up to 2.6.4 1992 - December 1998
Anne 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 1.3
August 2000
Contributors to RasTop Manual
Roger Sayle
Margaret Wong
Eric Martz
William McClure
Herbert J. Bernstein
Philippe Valadon
 
Contact the author

RasTop 1.3 Help

Molecular Graphics Visualization Tool
Philippe Valadon, August 2000

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Welcome to RasTop molecular visualization software. RasTop is a graphical interface to RasMol adapted for Windows platform. This site contains all the information needed to get, run, use, contribute, and/or modify RasTop. This site also contains the information needed to run and use RasMol, version 2.7.1, developed initially by Roger Sayle, contributed in particular by Anne Muller, and under current development by Herbert J. Berstein. Many thanks to these people for giving RasMol freely to the community. It is a wonderful experience to enter RasMol project and I encourage all of you to continue the work and have the same pleasure that I had during the building of RasTop. 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 entire 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.


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 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 sets under an extended script format called RSM script.

Along its development, a few new capabilities were added: 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.

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 and be sure that you read the entire NOTICE before using RasTop. RasTop makes an extended use of memory, especially if you open several molecular files at the same time. Please report any strange behaviors and bugs.

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

RasTop is an open source; everybody is welcome to contribute to its development, but, like RasMol 2.7.1., certain restrictions apply. Read about restrictions applying on using the source in the NOTICE.


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 labeled 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.

Note that RasMol 2.7.1 is open source, but is not in the public domain. Certain conditions apply to users and to developers to ensure that RasMol 2.7.1 program and all programs derived from it remain open source. Read the complete Notice applying for RasMol.


About this Site

RasTop 1.3 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 'default.html'. You can also link RasTop directly to this site in the preferences.

YOU DO NOT NEED A NETWORK CONNECTION OR A WEB ACCESS TO VIEW THIS SITE.

 

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Last revision: September 17, 2000