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| Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual| Release README |

README
RasMol 2.7.1

RasMol
 
  Version   MAC PPC
binaries
  MSWIN
binaries
RasWin
Help File
  LINUX
binaries
RasMol
Help File
 
2.7.1 8     32 8 raw gz 8 16 32 raw gz
2.7.1.1 8     32 8 raw gz 8 16 32 raw gz
2.7.2 8     32 8 raw gz 8 16 32 raw gz
2.7.2.1 8     32 8 raw gz 8 16 32 raw gz
 
See Source Code and Binaries for more.

Molecular Graphics Visualisation Tool
22 June 1999

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

Version 2.7.0, 2.7.1 Mods 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

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.

Documentation Last Updated 5 July 1999
Edited by Herbert J. Bernstein and Frances C. Bernstein

Translation of RasMol 2.7.1 Manual into Spanish

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 (Departamento de Bioquímica y Biología Molecular. Universidad de Granada. España (jmfernan@ugr.es))


Test Version of Next Release Available

A preliminary release of RasMol 2.7.2 is available at:

http://www.bernstein-plus-sons.com/software/RasMol_2.7.2

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


RasTop 1.3 Available

RasTop by P. Valadon is a graphical interface to RasMol adapted for Windows platform, i.e. RasTop is a GUI front end for RasWin.

  • RasTop -- GUI front end for RasWin (RasTop 1.3)

    IMPORTANT - Copying and Distribution

    This version is based on RasMol version 2.6_CIF.2, on RasMol version 2.6x1 and on RasMol version 2.6.4. Please read the file NOTICE for important notices which apply to this package. If you are not going to make changes to RasMol, you are not only permitted to freely make copies and distribute them, you are encouraged to do so, provided you do the following:

    If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following:

    This version of RasMol is not in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol.


    Contents


    Introduction

    This posting is to announce the release of RasMol version 2.7.1, which makes the following changes to RasMol 2.7.0:

    RasMol version 2.7.0.1 was a technically minor, but operationally critical upgrade to version 2.7.0, correcting a serious error in the selection logic introduced in the process of merging versions to create version 2.7.0.

    RasMol version 2.7.0 combined Roger Sayle's version 2.6.4 with Herbert Bernstein's CIF modified version 2.6_CIF(Rev 2) and with Arne Mueller's version 2.6x1. This combined version allows selection by alternate conformers as well as by models, production of Ramachandran printer plots (as in F. Bernstein's fisipl), and access to A. Mueller's POVray output as POVray3 in addition to the existing POVray version 2 output. (POVray3 should not be used in the PC or Mac version, yet).

    RasMol version 2.6x1 was an upgrade to RasMol by Arne Mueller to add code to allow listing of information about the chains, groups or atoms in a selection, listing of phi-psi, allow selection by cis angle cutoff, and to provide a POV-Ray version 3 output.

    RasMol version 2.6.4 was a major code cleanup and reorganization by Roger Sayle, dropping obsolete non-ANSI C options and providing speed improvments.

    RasMol version 2.6_CIF(Rev 2) added pre-compiled binaries for OpenVMS 7.1 (DEC Alpha) and OpenVMS 6.2 (DEC VAX) and replaced the binary for 68K Apple MacIntoshes in RasMol version 2.6_CIF(Rev 1).

    Rasmol version 2.6_CIF(Rev 1) was a minor update to RasMol version 2.6_CIF, which added support for alternate conformer coloring of small molecule CIFs, using _atom_site_disorder_group, recognizes requests for bonds which have neither atom names nor atom numbers, ensures zapping of existing bonds when connect command is used.

    RasMol version 2.6_CIF added several new features to RasMol:

    This version is available for the Apple Macintosh and PowerMac in addition to UNIX, VMS and Microsoft Windows versions. However, because of limitations in the memory management under MacOS, very large multiple NMR model datasets are not supported on the Mac or PowerMac at this time.

    For a complete list of changes from RasMol 2.6 refer to the distribution's "ChangeLog".

    For installation instructions see "INSTALL".

    For a list of open issues in this version, see "TODO". Roger Sayle's prior list of pending projects is in "PROJECTS".

    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 has 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.

    RasMol will 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.

    As of this writing (24 September 1999), this version has been built for Linuxppc, i386 RedHat 6.0 Linux, SGI, DEC OpenVMS, Mac, IBM PC under Windows 95 and IBM RS/6000's under AIX 4.3.2. Reports of builds and/or problems on other platforms appreciated. Our thanks to David Atkinson at BU, Bob Sweet at BNL, Helen Berman at John Westbrook at Rutgers for access to computers used for some of the compilations for this release. Our thanks to Jan Boshoff for the 8-bit AIX 4.3.2 binary. Additional thanks to David Atkinson for contributing the compiled Alpha Dunix binaries, and to Jon Bruno for the compiled i386 RedHat 6.0 Linux binaries.


    Source Code and Binaries

    The complete source code and user documentation of RasMol 2.7.1 may be obtained by anonymous FTP at:

    ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.tar.gz

    or on the web at:

    http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.tar.gz

    The source code and documentation are stored in several files appropriate for the receiving operating system. Please read the "README" file in the distribution directory. See the table below for appropriate binaries. Mac and Windows binaries are no longer included on the tar. Unix and VMS users should retrieve the same file for source code and documentation, and one or more of the following pre-compiled binaries: WARNING: ALL binaries are gzipped!!!

    System Binary Help Files
    Linux (RedHat 6.0, i386): RasMol.LINUX/RedHat_6.0/i386/rasmol_8BIT.gz rasmol.hlp.gz
      RasMol.LINUX/RedHat_6.0/i386/rasmol_16BIT.gz rasmol.hlp.gz
      RasMol.LINUX/RedHat_6.0/i386/rasmol_32BIT.gz rasmol.hlp.gz
         
    RS/6000 (AIX 4.3.2): RasMol.RS6K/rasmol_8BIT.gz doc/rasmol.hlp.gz
         
    SGI (IRIX 5.3): RasMol.SGI/IRIX_5.3/rasmol_8BIT.gz rasmol.hlp.gz
      RasMol.SGI/IRIX_5.3/rasmol_16BIT.gz rasmol.hlp.gz
      RasMol.SGI/IRIX_5.3/rasmol_32BIT.gz rasmol.hlp.gz
         
    SGI (IRIX 6.4): RasMol.SGI/IRIX_6.4/rasmol_8BIT.gz rasmol.hlp.gz
      RasMol.SGI/IRIX_6.4/rasmol_16BIT.gz rasmol.hlp.gz
      RasMol.SGI/IRIX_6.4/rasmol_32BIT.gz rasmol.hlp.gz
         
    Alpha (OpenVMS 7.1): RasMol.DEC/OpenVMS_7.1/rasmol_8bit.exe.gz rasmol.hlp.gz
      RasMol.DEC/OpenVMS_7.1/rasmol_16bit.exe.gz rasmol.hlp.gz
      RasMol.DEC/OpenVMS_7.1/rasmol_32bit.exe.gz rasmol.hlp.gz
         
    Alpha (Dunix 4.0D): RasMol.DEC/Dunix_4.0D/rasmol_8bit.gz rasmol.hlp.gz
      RasMol.DEC/Dunix_4.0D/rasmol_32bit.gz rasmol.hlp.gz
         
    VAX (OpenVMS 6.2): RasMol.DEC/OpenVMS_6.2/rasmol_8bit.exe.gz rasmol.hlp.gz
      RasMol.DEC/OpenVMS_6.2/rasmol_16bit.exe.gz rasmol.hlp.gz
      RasMol.DEC/OpenVMS_6.2/rasmol_32bit.exe.gz rasmol.hlp.gz
         
    Mac: RasMac_FAT_8BIT.bin.gzrasmol.hlp.gz
      RasMac_PPC_8BIT.bin.gz
      RasMac_68K_8BIT.bin.gz
      RasMac_FAT_32BIT.bin.gz
      RasMac_PPC_32BIT.bin.gz
      RasMac_68K_32BIT.bin.gz
         
    Windows: RasWin.exe.gz rasmol.hlp.gz, raswin.hlp.gz

    For those who have difficulty downloading "gzipped" files, uncompressed files are available:
    System Binary Help Files
    Linux (RedHat 6.0, i386): RasMol.LINUX/RedHat_6.0/i386/rasmol_8BIT rasmol.hlp
      RasMol.LINUX/RedHat_6.0/i386/rasmol_16BIT rasmol.hlp
      RasMol.LINUX/RedHat_6.0/i386/rasmol_32BIT rasmol.hlp
         
    RS/6000 (AIX 4.3.2): RasMol.RS6K/rasmol_8BIT rasmol.hlp
         
    SGI (IRIX 5.3): RasMol.SGI/IRIX_5.3/rasmol_8BIT rasmol.hlp
      RasMol.SGI/IRIX_5.3/rasmol_16BIT rasmol.hlp
      RasMol.SGI/IRIX_5.3/rasmol_32BIT rasmol.hlp
         
    SGI (IRIX 6.4): RasMol.SGI/IRIX_6.4/rasmol_8BIT rasmol.hlp
      RasMol.SGI/IRIX_6.4/rasmol_16BIT rasmol.hlp
      RasMol.SGI/IRIX_6.4/rasmol_32BIT rasmol.hlp
         
    Alpha (OpenVMS 7.1): RasMol.DEC/OpenVMS_7.1/rasmol_8bit.exe rasmol.hlp
      RasMol.DEC/OpenVMS_7.1/rasmol_16bit.exe rasmol.hlp
      RasMol.DEC/OpenVMS_7.1/rasmol_32bit.exe rasmol.hlp
         
    Alpha (Dunix 4.0D): RasMol.DEC/Dunix_4.0D/rasmol_8bit rasmol.hlp
      RasMol.DEC/Dunix_4.0D/rasmol_32bit rasmol.hlp
         
    VAX (OpenVMS 6.2): RasMol.DEC/OpenVMS_6.2/rasmol_8bit.exe rasmol.hlp
      RasMol.DEC/OpenVMS_6.2/rasmol_16bit.exe rasmol.hlp
      RasMol.DEC/OpenVMS_6.2/rasmol_32bit.exe rasmol.hlp
         
    Mac: RasMac_FAT_8BIT.binrasmol.hlp
      RasMac_PPC_8BIT.bin
      RasMac_68K_8BIT.bin
      RasMac_FAT_32BIT.bin
      RasMac_PPC_32BIT.bin
      RasMac_68K_32BIT.bin
         
    Windows: RasWin.exe rasmol.hlp, raswin.hlp

    You will need both an appropriate binary and a copy of rasmol.hlp for each system, and, under Windows, a copy of raswin.hlp for the WinHelp sub-system.

    Please remember to use "binary" mode when transferring these files between systems. Check that the file size is the same before and after transfer.

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


    RasTop 1.3 Features

    RasTop is a graphical interface to RasMol adapted for Windows platform, i.e. RasTop is a GUI front end for RasWin.

    RasTop offers 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 atom sets under an extended script format called RSM script.

    During its development, a few new capabilities were added: back clipping, 32-bit output under Windows, full centring command either on a selected atom or to the origin, variation of depthcue in slab mode, and a colouring command, shadepower, which generates new metal-like surfaces.

    RasTop allows several molecules to be opened at the same time (on different windows) and provides limited editing of the molecular file.

    RasTop 1.3, like RasMol 2.7.1, contains a lot of new code. Under its current version, RasTop 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.

    Released by P. Valadon, 27 August 2000


    | Copying and Distribution | Contents | Installation Instructions |
    | Changes | Things To Do | Introduction | Source Code and Binaries | | RasMol Manual | Spanish Translation of RasMol Manual| Release README |

    Updated 17 April 2001.
    Herbert J. Bernstein
    Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
    yaya@bernstein-plus-sons.com
    +1-631-286-1339