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| OpenRasMol | 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 2.7.1.1

RasMol
***NEW*** HPUX_11, Solaris 2.5 Binaries available. ***NEW***
  Version   MAC PPC
binaries
  MSWIN
binaries
RasWin
Help File
  LINUX
binaries
RasMol
Help File
  MORE ...  
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 HPUX 11   Solaris 2.5
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 HPUX 11   Solaris 2.5   OpenVMS  SGI
 
See Source Code and Binaries for more.

Molecular Graphics Visualisation Tool
21 January 2001

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, 2.7.1.1 Mods by Herbert J. Bernstein
Bernstein + Sons, P.O. Box 177, Bellport, NY, USA,
2.7.0 March 1999, 2.7.1 June 1999, 2.7.1.1 January 2001
Copyright © Herbert J. Bernstein 1998-2001

Translations of most of the RasMol messages into Spanish contributed by Fernando Gabriel Ranea (Laboratorio de Micología, Museo de Farmacobotánica, Facultad de Farmacia y Bioquímica. Universidad de Buenos Aires ( )

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 21 January 2001
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 ( 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.


Test Version of Next Release Available

RasMol 2.7.1.1 is an interim release for testing of the integration of multilingual capabilities into RasMol. These same mods will then be integrated with pending mods, and with the basic structure of RasMol 2.7.2 to create RasMol 2.7.2.1.

A preliminary release of RasMol 2.7.2 (without the multilingual capabilities) 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

    Note (1 May 2002): Compilations for Sun Solaris 2.5.1 (Sun OS 5.5.1) have been added.

    Note (19 Apr 2002): Post release patches to facilitate HPUX_11 binary builds have been included, and a full range of HPUX_11 binaries (both PARISC and IA64) have been made available. These patches will help RasMol in adapting to other 64-bit architectures. Our thanks to Gabriele Rearick of Hewlett Packard for her assistance and for making HP computers available for the builds. Gabriele Rearick has also provided a script, hp_supported.ksh, that may be used to identify the correct version of rasmol (PARISC or IA64) to run under HPUX on your system.

    This posting is to announce the release of RasMol version 2.7.1.1, which makes the following changes to RasMol 2.7.1:

    This is an interim release to facillitate testing of the new multilingual capabilities. Our thanks to Fernando Gabriel Ranea for doing the hard work of creating an initial Spanish translation of RasMol 2.7.1. We have created this new version to allow on-the-fly switching among languages. Use the command "Spanish" to request Spanish messages and menus, and "English" to return to the original English format. Corrections and translations for additional languages greatly appreciated.

    RasMol version 2.7.1, made the following changes to RasMol 2.7.0:

    • The ability to automatically mark non bonded atoms in wireframe and stick displays. Our thanks to R. Curtis Haltiwanger for suggesting this change.
    • The ability to use a proportionally spaced font and to draw labels with heavier strokes. Our thanks to Eric Martz for suggesting this change.
    • The ability to auto-recognize PDB vs. CIF and mmCIF datasets.
    • Extensive updating to the manual. Our thanks to William McClure, Margaret Wong, Eric Martz and Frances Bernstein.
    • Updating the canvas title with the PDB ID code and EXPDTA information, so models will be clearly distinguished from experimental data. Our thanks to Helen Berman for suggesting this change.
    • The ability to report coordinates.
    • Additions to the list of pre-defined colours.
    • Improved accuracy of coordinates in pseudo-PDB output.
    • Fixes to the centering logic.

    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:

    • Support for reading IUCr CIF and mmCIF format;
    • Coloring for alternate conformers and multiple NMR models;
    • Display of all NMR models in a data set.

    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 (7 May 2002), this version has been built for i586 Mandrake 7.2 Linux, Mac, IBM PC under Windows 95/98, SGI IRIX 6.4, HPUX 11 (PARISC and IA64), and Sun Solaris 2.5.1. Reports of builds and/or problems on other platforms appreciated. Our thanks to Gabriele Rearick of HP Fort Collins for access to the necessary HP systems. Our thanks to Edward Hawrot of Brown University for donation of a Sparcserver 670 MP to the Accessible Retired Computers in Biology (ARCiB) project at Dowling College. The Sparcserver was used to compile the Solaris 2.5.1 binaries. Our thanks to the NSF for funding of the ARCiB project.


    Source Code and Binaries

    The complete source code and user documentation of RasMol 2.7.1.1 may be obtained by anonymous FTP at:

    ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.1.tar.gz

    or on the web at:

    http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1.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
    HPUX: HPUX 11.00 (PARISC), 8 bit display, 32 bit compilation, gzipped
    rasmol_8BIT_HPUX_PARISC_32.gz
    rasmol.hlp.gz
      HPUX 11.00 (PARISC), 8 bit display, 64 bit compilation, gzipped
    rasmol_8BIT_HPUX_PARISC_64.gz
    rasmol.hlp.gz
      HPUX 11.00 (PARISC), 16 bit display, 32 bit compilation, gzipped
    rasmol_16BIT_HPUX_PARISC_32.gz
    rasmol.hlp.gz
      HPUX 11.00 (PARISC), 16 bit display, 64 bit compilation, gzipped
    rasmol_16BIT_HPUX_PARISC_64.gz
    rasmol.hlp.gz
      HPUX 11.00 (PARISC), 32 bit display, 32 bit compilation, gzipped
    rasmol_32BIT_HPUX_PARISC_32.gz
    rasmol.hlp.gz
      HPUX 11.00 (PARISC), 32 bit display, 64 bit compilation, gzipped
    rasmol_32BIT_HPUX_PARISC_64.gz
    rasmol.hlp.gz
         
    Gabriele Rearick has provided a script, hp_supported.ksh, that may be used to identify the correct version of rasmol (PARISC or IA64) to run under HPUX on your system.
         
      HPUX 11.20 (IA64), 8 bit display, 32 bit compilation, gzipped
    rasmol_8BIT_HPUX_IA64_32.gz
    rasmol.hlp.gz
      HPUX 11.20 (IA64), 8 bit display, 64 bit compilation, gzipped
    rasmol_8BIT_HPUX_IA64_64.gz
    rasmol.hlp.gz
      HPUX 11.20 (IA64), 16 bit display, 32 bit compilation, gzipped
    rasmol_16BIT_HPUX_IA64_32.gz
    rasmol.hlp.gz
      HPUX 11.20 (IA64), 16 bit display, 64 bit compilation, gzipped
    rasmol_16BIT_HPUX_IA64_64.gz
    rasmol.hlp.gz
      HPUX 11.20 (IA64), 32 bit display, 32 bit compilation, gzipped
    rasmol_32BIT_HPUX_IA64_32.gz
    rasmol.hlp.gz
      HPUX 11.20 (IA64), 32 bit display, 64 bit compilation, gzipped
    rasmol_32BIT_HPUX_IA64_64.gz
    rasmol.hlp.gz
         
    Sun: Solaris 2.5.1/SunOS 5.5.1 (sparc) 8 bit display, gcc compilation, gzipped
    rasmol_8BIT_gcc.gz
    rasmol.hlp.gz
      Solaris 2.5.1/SunOS 5.5.1 (sparc) 16 bit display, gcc compilation, gzipped
    rasmol_16BIT_gcc.gz
    rasmol.hlp.gz
      Solaris 2.5.1/SunOS 5.5.1 (sparc) 32 bit display, gcc compilation, gzipped
    rasmol_32BIT_gcc.gz
    rasmol.hlp.gz
         
    Linux: Linux (Mandrake 7.2, i586), 8 bit display, gzipped
    rasmol_8BIT.gz
    rasmol.hlp.gz
      Linux (Mandrake 7.2, i586), 16 bit display, gzipped
    rasmol_16BIT.gz
    rasmol.hlp.gz
      Linux (Mandrake 7.2, i586), 32 bit display, gzipped
    rasmol_32BIT.gz
    rasmol.hlp.gz
         
    SGI: SGI (IRIX 6.4), 8 bit display, gzipped
    rasmol_8BIT.gz
    rasmol.hlp.gz
      SGI (IRIX 6.4), 16 bit display, gzipped
    rasmol_16BIT.gz
    rasmol.hlp.gz
      SGI (IRIX 6.4), 32 bit display, gzipped
    rasmol_32BIT.gz
    rasmol.hlp.gz
         
    Mac: Macintosh (MacOS 7.6-9.1), 8 bit display, PPC or 68K, CodeWarrior 5 compilation, MacBinary, gzipped
    RasMac_FAT_8BIT.bin.gz
    rasmol.hlp.gz
      Macintosh (MacOS 7.6-9.1), 8 bit display, PPC, CodeWarrior 5 compilation, MacBinary, gzipped
    RasMac_PPC_8BIT.bin.gz

      Macintosh (MacOS 7.6-9.1), 8 bit display, 68K, CodeWarrior 5 compilation, MacBinary, gzipped
    RasMac_68K_8BIT.bin.gz

      Macintosh (MacOS 7.6-9.1), 32 bit display, PPC or 68K, CodeWarrior 5 compilation, MacBinary, gzipped
    RasMac_FAT_32BIT.bin.gz

      Macintosh (MacOS 7.6-9.1), 32 bit display, PPC, CodeWarrior 5 compilation, MacBinary, gzipped
    RasMac_PPC_32BIT.bin.gz

      Macintosh (MacOS 7.6-9.1), 32 bit display, 68K, CodeWarrior 5 compilation, MacBinary, gzipped
    RasMac_68K_32BIT.bin.gz

         
    Windows: PC clone (MS Windows 95, 98) CodeWarrior 5 compilation
    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
    HPUX: HPUX 11.00 (PARISC), 8 bit display, 32 bit compilation
    rasmol_8BIT_HPUX_PARISC_32
    rasmol.hlp
      HPUX 11.00 (PARISC) 8 bit display, 64 bit compilation
    rasmol_8BIT_HPUX_PARISC_64
    rasmol.hlp
      HPUX 11.00 (PARISC) 16 bit display, 32 bit compilation
    rasmol_16BIT_HPUX_PARISC_32
    rasmol.hlp
      HPUX 11.00 (PARISC) 16 bit display, 64 bit compilation
    rasmol_16BIT_HPUX_PARISC_64
    rasmol.hlp
      HPUX 11.00 (PARISC) 32 bit display, 32 bit compilation
    rasmol_32BIT_HPUX_PARISC_32
    rasmol.hlp
      HPUX 11.00 (PARISC) 32 bit display, 64 bit compilation
    rasmol_32BIT_HPUX_PARISC_64
    rasmol.hlp
         
      HPUX 11.20 (IA64), 8 bit display, 32 bit compilation
    rasmol_8BIT_HPUX_IA64_32
    rasmol.hlp
      HPUX 11.20 (IA64), 8 bit display, 64 bit compilation
    rasmol_8BIT_HPUX_IA64_64
    rasmol.hlp
      HPUX 11.20 (IA64), 16 bit display, 32 bit compilation
    rasmol_16BIT_HPUX_IA64_32
    rasmol.hlp
      HPUX 11.20 (IA64), 16 bit display, 64 bit compilation
    rasmol_16BIT_HPUX_IA64_64
    rasmol.hlp
      HPUX 11.20 (IA64), 32 bit display, 32 bit compilation
    rasmol_16BIT_HPUX_IA64_32
    rasmol.hlp
      HPUX 11.20 (IA64), 32 bit display, 64 bit compilation
    rasmol_16BIT_HPUX_IA64_64
    rasmol.hlp
         
    Sun: Solaris 2.5.1/SunOS 5.5.1 (sparc) 8 bit display, gcc compilation
    rasmol_8BIT_gcc
    rasmol.hlp
      Solaris 2.5.1/SunOS 5.5.1 (sparc) 16 bit display, gcc compilation
    rasmol_16BIT_gcc
    rasmol.hlp
      Solaris 2.5.1/SunOS 5.5.1 (sparc) 32 bit display, gcc compilation
    RasMol.SUN/Solaris_2.5.1/sparc/rasmol_32BIT_gcc
    rasmol.hlp
         
    Linux: Linux (Mandrake 7.2, i586), 8 bit display
    rasmol_8BIT
    rasmol.hlp
      Linux (Mandrake 7.2, i586), 16 bit display
    rasmol_16BIT
    rasmol.hlp
      Linux (Mandrake 7.2, i586), 32 bit display
    rasmol_32BIT
    rasmol.hlp
         
    SGI: SGI (IRIX 6.4), 8 bit display
    rasmol_8BIT
    rasmol.hlp
      SGI (IRIX 6.4), 16 bit display
    rasmol_16BIT
    rasmol.hlp
      SGI (IRIX 6.4), 32 bit display
    rasmol_32BIT
    rasmol.hlp
         
    Mac: Macintosh (MacOS 7.6-9.1), 8 bit display, PPC or 68K, CodeWarrior 5 compilation, MacBinary
    RasMac_FAT_8BIT.bin
    rasmol.hlp
      Macintosh (MacOS 7.6-9.1), 8 bit display, PPC, CodeWarrior 5 compilation, MacBinary
    RasMac_PPC_8BIT.bin

      Macintosh (MacOS 7.6-9.1), 8 bit display, 68K, CodeWarrior 5 compilation, MacBinary
    RasMac_68K_8BIT.bin

      Macintosh (MacOS 7.6-9.1), 32 bit display, PPC or 68K, CodeWarrior 5 compilation, MacBinary
    RasMac_FAT_32BIT.bin

      Macintosh (MacOS 7.6-9.1), 32 bit display, PPC, CodeWarrior 5 compilation, MacBinary
    RasMac_PPC_32BIT.bin

      Macintosh (MacOS 7.6-9.1), 32 bit display, 68K, CodeWarrior 5 compilation, MacBinary
    RasMac_68K_32BIT.bin

         
    Windows: PC clone (MS Windows 95, 98) CodeWarrior 5 compilation
    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


    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


    | OpenRasMol | 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 13 January 2003.
    Herbert J. Bernstein
    Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA

    +1-631-286-1339