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README
RasMol 2.7.4.2

       RasMol       

Molecular Graphics Visualisation Tool
19 November 2007 (rev. 17 March 2008)

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
AuthorVersion, DateCopyright
Arne MuellerRasMol 2.6x1 May 1998© Arne Mueller 1998
Gary Grossman and
Marco Molinaro
RasMol 2.5-ucb November 1995
RasMol 2.6-ucb November 1996
© UC Regents/ModularCHEM
Consortium 1995, 1996
Philippe ValadonRasTop 1.3 August 2000© Philippe Valadon 2000
Herbert J. BernsteinRasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999
RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000
RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
RasMol 2.7.3.1 Apr 06
RasMol 2.7.4 Nov 07
RasMol 2.7.4.1 Jan 08
RasMol 2.7.4.2 Mar 08
© Herbert J. Bernstein 1998-2008

RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department of Energy. RasMol 2.7.4 incorporates changes by G. Todorov, Nan Jia, N. Darakev, P. Kamburov, G. McQuillan, J. Jemilawon. Work on RasMol 2.7.4 supported in part by grant 1R15GM078077-01 from the National Institute of General Medical Sciences (NIGMS). The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding organizations.

and Incorporating Translations by
AuthorItemLanguage
Isabel Serván Martínez,
José Miguel Fernández Fernández
2.6 ManualSpanish
José Miguel Fernández Fernández2.7.1 ManualSpanish
Fernando Gabriel Ranea2.7.1 menus and messagesSpanish
Jean-Pierre Demailly2.7.1 menus and messagesFrench
Giuseppe Martini, Giovanni Paolella,
A. Davassi, M. Masullo, C. Liotto
2.7.1 menus and messages
2.7.1 help file
Italian
G. Pozhvanov2.7.3 menus and messagesRussian
G. Todorov2.7.3 menus and messagesBulgarian
Nan Jia, G. Todorov2.7.3 menus and messagesChinese
Mamoru Yamanishi, Katajima Hajime2.7.3 menus and messagesJapanese

This Release by
Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA

Copyright © Herbert J. Bernstein 1998-2008

The original RasMol manual was created by Roger Sayle. In July 1996, Dr. Margaret Wong of the Chemistry Department, Swinburne University of Technology, Australia, made extensive revisions to the RasMol 2.5 manual to accurately reflect the operation of RasMol 2.6. Eric Martz of the University of Massachusetts made further revisions. In May 1997, William McClure of Carnegie Mellon University reorganized the HTML version of the manual into multiple sections which could be downloaded quickly and added use of frames. Portions of the 2.7.1 version of the RasMol manual were derived with permission from William McClure's version using Roger Sayle's rasmol.doc for version 2.6.4 as the primary source. Changes were made in August 2000 for RasMol version 2.7.2, January 2001 for RasMol version 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and February 2005 for RasMol version 2.7.3.

Documentation Last Updated 12 November 2007
Edited by Herbert J. Bernstein and Frances C. Bernstein

Translations

Thanks to the efforts of José Miguel Fernández Fernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada. España (jmfernan@ugr.es)) a translation of the Manual for Rasmol version 2.7.1 into Spanish is now available. La traducción española del manual de la versión de la Dra. Wong revisada por Eric Martz fue realizada por Isabel Serván Martínez y José Miguel Fernández Fernández. La actual traducción del Manual de RasMol 2.7.1 ha sido realizada usando como base la anterior de RasMol 2.6 por  José Miguel Fernández Fernández.

Thanks to translations by Fernando Gabriel Ranea in late 2000 and early 2001, RasMol is now capable of rendering most menu items and messages in Spanish. Jean-Pierre Demailly provided French translations of menus and messages in January 2001. Giuseppe Martini and Giovanni Paolella with contributions by A. Davassi, M. Masullo and C. Liotto provided Italian translations of menus and messages in March 2001.


THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******


IMPORTANT - Copying and Distribution

This version is based directly on RasMol version 2.7.4, on RasMol version 2.7.3.1, on RasMol vesion 2.7.3, on RasMol version 2.7.2.1.1, on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version 2.6.4, and RasMol 2.5-ucb and 2.6-ucb.

Please read the file NOTICE for important notices which apply to this package and for license terms (GPL or RASLIC).


Contents


Introduction

This posting is made to announce the releases of RasMol version 2.7.4.2. This release is based on RasMol 2.7.4 and RasMol 2.7.4.1 and RasMol 2.7.3.1, the final reference release for the 2.7.3 series. The changes from the 2.7.3.1 release to the 2.7.4.1 release include:

The changes from the 2.7.4.1 release to the 2.7.4.2 release include For more detail on these and earlier changes, see the Change Log.

This version is available for MS Windows and various unix-systems. As binaries become available, they will be released on http://blondie.dowling.edu/projects/rasmol and http://www.sourceforge.net/projects/openrasmol.

For installation instructions see "INSTALL".

For a list of open issues in this version, see "TODO".

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 original program was been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structures Group at Glaxo Research and Development, Greenford, UK.

RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations. Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format, CHARMm format, MOPAC format, CIF format and mmCIF format files. If connectivity information and/or secondary structure information is not contained in the file this is calculated automatically. The loaded molecule may be shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon trace, spacefilling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface. 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 displayed and coloured independently of the rest of the molecule or shown in different representations simultaneously. The space filling spheres can even be shadowed. The displayed molecule may be rotated, translated, zoomed, z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dials box. RasMol can read a prepared list of commands from a `script' file (or via interprocess 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 both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.

Versions of RasMol have run on a wide range of architectures and systems including SGI, sun4, sun3, sun386i, SGI, DEC, HP and E&S workstations, IBM RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC Windows). UNIX and VMS versions require an 8bit, 24bit or 32bit X Windows frame buffer (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory rendering (via the XInput and MIT-SHM extensions) if available.

Reports of builds and/or problems on various platforms appreciated.


Source Code and Binaries

The complete source code and user documentation of RasMol 2.7.4 may be obtained from http://blondie.dowling.edu/projects/rasmol and http://www.sourceforge.net/projects/openrasmol. and by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.4.2.tar.gz

or on the web at:

http://www.bernstein-plus-sons.com/software/RasMol_2.7.4.2.tar.gz

As compiled version become available, they will be posted at http://blondie.dowling.edu/projects/rasmol and http://www.sourceforge.net/projects/openrasmol.

Any comments, suggestions or questions about this modified version of RasMol should be directed to rasmol@bernstein-plus-sons.com.

| OpenRasMol | Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual | Italian Translation of RasMol 2.7.1 Help File |
| Donate to Support RasMol | Release README | Register your RasMol |

Updated 4 February 2008.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA