                           Installation Instructions
                                  RasMol 2.7.5
                     Molecular Graphics Visualisation Tool
                        3 June 2009 (rev. 17 July 2009)

                       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 (c) Roger Sayle 1992-1999

                              and Based on Mods by

+------------------------------------------------------------------------------+
| Author            | Version, Date        | Copyright                         |
|-------------------+----------------------+-----------------------------------|
| Arne Mueller      | RasMol 2.6x1 May     | (c) Arne Mueller 1998             |
|                   | 1998                 |                                   |
|-------------------+----------------------+-----------------------------------|
| Gary Grossman and | RasMol 2.5-ucb       | (c) UC Regents/ModularCHEM        |
| Marco Molinaro    | November 1995        | Consortium 1995, 1996             |
|                   | RasMol 2.6-ucb       |                                   |
|                   | November 1996        |                                   |
|-------------------+----------------------+-----------------------------------|
| Philippe Valadon  | RasTop 1.3 August    | (c) Philippe Valadon 2000         |
|                   | 2000                 |                                   |
|-------------------+----------------------+-----------------------------------|
| Herbert J.        | RasMol 2.7.0 March   | (c) Herbert J. Bernstein          |
| Bernstein         | 1999                 | 1998-2008                         |
|                   | 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 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                   |                                   |
|                   | RasMol 2.7.5 June    |                                   |
|                   | 2009                 |                                   |
|                   | RasMol 2.7.5.1 July  |                                   |
|                   | 2009                 |                                   |
+------------------------------------------------------------------------------+

   RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
   and L. Andrews (via the neartree package). Work on RasMol 2.7.5 supported
   in part by grant 1R15GM078077-01 from the National Institute of General
   Medical Sciences (NIGMS), U.S. National Institutes of Health and by grant
   ER63601-1021466-0009501 from the Office of Biological & Environmental
   Research (BER), Office of Science, U. S. Department of Energy. RasMol
   2.7.4 incorporated changes by G. Todorov, Nan Jia, N. Darakev, P.
   Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol 2.7.4 supported
   in part by grant 1R15GM078077-01 from the NIGMS/NIH and grant
   ER63601-1021466-0009501 from BER/DOE. 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
   BER/DOE. The content is solely the responsibility of the authors and does
   not necessarily represent the official views of the funding organizations.

   The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
   Teemu Ikonen.

                       and Incorporating Translations by

+-----------------------------------------------------------------------------+
| Author                               | Item                     | Language  |
|--------------------------------------+--------------------------+-----------|
| Isabel Servan Martinez,              | 2.6 Manual               | Spanish   |
| Jose Miguel Fernandez Fernandez      |                          |           |
|--------------------------------------+--------------------------+-----------|
| Jose Miguel Fernandez Fernandez      | 2.7.1 Manual             | Spanish   |
|--------------------------------------+--------------------------+-----------|
| Fernando Gabriel Ranea               | 2.7.1 menus and messages | Spanish   |
|--------------------------------------+--------------------------+-----------|
| Jean-Pierre Demailly                 | 2.7.1 menus and messages | French    |
|--------------------------------------+--------------------------+-----------|
| Giuseppe Martini, Giovanni Paolella, | 2.7.1 menus and messages | Italian   |
| A. Davassi, M. Masullo, C. Liotto    | 2.7.1 help file          |           |
|--------------------------------------+--------------------------+-----------|
| G. Pozhvanov                         | 2.7.3 menus and messages | Russian   |
|--------------------------------------+--------------------------+-----------|
| G. Todorov                           | 2.7.3 menus and messages | Bulgarian |
|--------------------------------------+--------------------------+-----------|
| Nan Jia, G. Todorov                  | 2.7.3 menus and messages | Chinese   |
|--------------------------------------+--------------------------+-----------|
| Mamoru Yamanishi, Katajima Hajime    | 2.7.3 menus and messages | Japanese  |
+-----------------------------------------------------------------------------+

                                This Release by
   Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
                          yaya@bernstein-plus-sons.com
                  Copyright (c) Herbert J. Bernstein 1998-2009

   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 19 July 2009
            Edited by Herbert J. Bernstein and Frances C. Bernstein

                                  Translations

   Thanks to the efforts of Jose Miguel Fernandez Fernandez (Departamento de
   Bioquimica y Biologia Molecular. Universidad de Granada. Espana
   (jmfernan@ugr.es)) a translation of the Manual for Rasmol version 2.7.1
   into Spanish is now available. La traduccion espanola del manual de la
   version de la Dra. Wong revisada por Eric Martz fue realizada por Isabel
   Servan Martinez y Jose Miguel Fernandez Fernandez. La actual traduccion
   del Manual de RasMol 2.7.1 ha sido realizada usando como base la anterior
   de RasMol 2.6 por  Jose Miguel Fernandez Fernandez.

   Thanks to translations by Fernando Gabriel Ranea <davinci@dinamica.com.ar>
   in late 2000 and early 2001, RasMol is now capable of rendering most menu
   items and messages in Spanish. Jean-Pierre Demailly
   <Jean-Pierre.Demailly@ujf-grenoble.fr> provided French translations of
   menus and messages in January 2001. Giuseppe Martini
   <martini@iigb.na.cnr.it> and Giovanni Paolella <paolella@dbbm.unina.it>
   with contributions by A. Davassi, M. Masullo and C. Liotto provided
   Italian translation 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 2.7.4.2, on RasMol
   version 2.7.4.1, 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).

     ----------------------------------------------------------------------

  Obtaining RasMol v2.7.5

   In order to install RasMol, you may start with a compiled binary or work
   from the source code.

   The complete source code and user documentation of RasMol 2.7.5 may be
   obtained from http://blondie.dowling.edu/projects/rasmol and
   http://blondie.dowling.edu/projects/rasmol. and by anonymous FTP at:

   ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.5.tar.gz

   or on the web at:

   http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.tar.gz

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

   To transfer by anonymous ftp, type "ftp ftp.bernstein-plus-sons.com" on
   the command line. Several seconds later you'll be prompted for a username.
   Use the username "anonymous" and when asked for a password enter your
   e-mail address. Once logged in, type the command "cd software/rasmol" to
   change the directory to /software/rasmol and then type "binary" to avoid
   corrupting the files during the transfer. For each file you wish to
   transfer, type "get <filename>" and when you've finished type "quit". If
   these files are subsequently transfered to other machines, please remember
   to transfer them in BINARY mode. The file sizes should be identical before
   and after the transfer.

   NOTE: The Mac uses the "carriage return" character to signify the end of a
   line, while UNIX machines use a "linefeed". If a file is transfered
   between these two machines in "ASCII" mode all such characters are
   exchanged, thereby corrupting the archive. Please ensure that you type the
   FTP command "binary" before you transfer the file, indicating that the
   file should be transfered without translation.

   If you wish to start from source code, you will need a RasMol source kit,
   and you may need one or more external packages that are not part of
   RasMol, but which are used by RasMol.

   To build/rebuild RasMol 2.7.5 on any platform, you'll need to transfer the
   following file:

   RasMol.tar.gz UNIX 'tar'ed 'gzip'ped archive containing the complete       
                 source code and documentation of the RasMol molecular        
                 graphics package.                                            

   To unpack the file on a UNIX machine type the command "gunzip
   RasMol.tar.gz" and then the command "tar -xvf RasMol.tar" to extract the
   files in a subdirectory under the current directory.

    *** IMPORTANT CHANGE IN INSTALLATION INSTRUCTIONS FOR RELEASE 2.7.5 ***

   You will either need to have the following packages installed in your
   system, or to ensure that the indicated defines are at the start
   Imakefile:

     * http://downloads.sf.net/neartree/NearTree-2.1.3.tar.gz or
       #define NEARTREE_LOCAL

     * http://downloads.sf.net/cqrlib/CQRlib-1.0.3.tar.gz or
       #define CQRLIB_LOCAL

       http://http://downloads.sf.net/cvector/CVector-1.0.3.tar.gz or
       #define CVECTOR_LOCAL

     * http://download.savannah.gnu.org/releases-noredirect/xforms/xforms-1.0.91.tar.gz
       or
       #define XFORMSLIB_LOCAL

     * http://downloads.sf.net/cbflib/CBFlib-0.8.1.tar.gz or
       #define CBFLIB_LOCAL

   In addition, depending on what has already been installed on your system,
   you may need one or more of certain font kits. These packages are not part
   of RasMol and normally whould be obtained from their primary web sites,
   but, for convenience in installing RasMol, they have been gathered in the
   external_packages module in the CVS and as the External_Packages release
   on http://blondie.dowling.edu/projects/rasmol and
   http://www.sourceforge.net/projects/openrasmol.

   These font kits are snapshots of the versions in use at the time of the
   build of RasMol 2.7.5. The primary developer web site for each package
   should be consulted for the latest versions. Because these kits may not be
   the same as later, standard versions that are used by the system, as a
   whole, scripts in RasMol that use thses kits (especially font kits) assume
   that each kit has been unpacked to a directory _within_ the RasMol build
   directory, at the same level as the src directory.

   For RasMol release 2.7.5 the package snapshots other than the font kits
   have been replaced by the table of downloads listed above.

   For building for MS Windows, do not try to use Visual Studio. Use MINGW
   instead.

   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.

   On an SGI, rename the appropriate binary as rasmol and copy it to
   /usr/local/bin/rasmol (or to some appropriate location specified by the
   environment variable PATH) and copy rasmol.hlp to
   /usr/local/lib/rasmol/rasmol.hlp (or to the location indicated by the
   environment variable RASMOLPATH)

     ----------------------------------------------------------------------

  Installing RasMol v2.7.5

    UNIX X11:

   If you are using a precompiled binary, see the instructions that are
   provided with the binary kit. In general, the binary kits for unix
   provided directly by this project are tarballs of the
   $HOME/lib/RasMol_2_7_5 created by running the script in
   src/rasmol_install.sh. The MS windows kit is a NSIS installer to be
   double-clicked after downloading.
    1. Fonts: Followling the instructions for your system, install whatever
       X11 font packages you need to the language variants of RasMol you
       intend to use. Almost all Unix variants come with the appropriate
       fonts for English, French, Spanish and Italian. There is an
       appropriate cyrillic font package, cyr-rfx-windows-1251-1.1, in
       external_packages. The Chinese and Japanese fonts in
       intlfonts-1.2.1.tar.gz in external_pakages seem to be satisfactory.
    2. In the RasMol src directory, either
          * Note for 64 bit CPUs: If you are building RasMol for a 64-bit CPU
            with a compiler that has a 64-bit long data type, you must either
            use the build_all.sh script, or manually

            #define _LONGLONG

            in rasmol.h
          * Modify the #defines in the file rasmol.h (see below) Note: IBMPC
            should not be defined.
          * either
               * Use the script rasmol_build_options.sh to build a new
                 Imakefile from Imakefile_base. The valid options are:
                 {--help|-h}
                 {--cbflib_local}
                 {--cqrlib_local}
                 {--cvector_local}
                 {--neartree_local}
                 {--xformslib_local}
                 {--use_xformslib}
                 {--use_gtk}
                 {--pixeldepth=32}
                 {--pixeldepth=16}
                 {--pixeldepth=8}
                 {--macosx_fink}

                 or
               * Edit Imakefile to change the desired options by hand. Use of
                 rasmol_build_options.sh is in general perferred
          * either
               * execute
                  &npsp;xmkmf
                 and
               * execute
                  &npsp;make rasmol
            or
               * edit the script build_all.sh
               * execute build_all.sh
            to build as many variants of rasmol as possible.
          * A common problem is that SUN OpenWindows keeps its include files
            in the directory /usr/openwin/include/X11, hence the compiler
            directive -I/usr/openwin/include must be added to CFLAGS.
          * A common problem on IBM RS6000s running AIX is that the MIT
            shared memory extensions to X windows are in the library
            -lXextSam, hence this must be added to the LIBS lines in either
            the Makefile or Imakefile.

    MS Windows:

            If you are using a precompiled binary, follow the instructions
            that come with the binary, but in general, you either need to
            place raswin.exe, rasmol.hlp and raswin.hlp into the directory
            from which you will run, or you need to execute the installer
            program by double clicking it.

            If you are building from source, you will need MINGW, not visual
            studio. CodeWarrior version 9 can also be used.

    Macintosh under OSX:

            Follow the instructions for unix and run under the X11 system. A
            pre-edited version of the build_all.sh script called
            build_MACOSX.sh is provided.

  COMPILATION DIRECTIVES

            The file rasmol.h contains a number of #define directives that
            control the runtime behaviour of the program. The following
            directives may be defined or undefined to suite the local site.

                         This determines whether RasMol will display and      
            THIRTYTWOBIT produce 8bit, 16bit or 32(24) bit output. By default 
            SIXTEENBIT   the symbol EIGHTBIT is defined producing images with 
            EIGHTBIT     up to 256 colours. This symbol must be defined if    
                         IBMPC is defined.                                    
            DIALBOX      This enables the use of a dials box, that is         
                         connected using the X Window System XInput           
                         extension. This option requires that the program be  
                         compiled with the Xi and Xext libraries. Note: libXi 
                         is called libXinput on some old machines, so         
                         requires the compiler option -lXinput!               
            MITSHM       This option enables the use of the X Window System   
                         MIT shared memory extension. This enables images to  
                         be displayed faster when RasMol and the X11 server   
                         are running on the same host. This option requires   
                         the program be compiled with the Xext library. On    
                         IBM RS6000s runnning AIX, MITSHM also requires the   
                         XextSam library (which requires changing the         
                         Makefile or Imakefile). This is now enabled by       
                         default. This should be disabled on E&S ESV          
                         workstations as MITSHM support is not provided as    
                         standard.                                            
            TERMIOS      This directive enables the command line processing   
                         on UNIXs that support the termios terminal handling  
                         routines. By leaving this symbol undefined, RasMol   
                         omits the interactive command line interface.        
                         Undefining is not recommended!                       
            SOCKETS      This directive enables the TCP/IP server             
                         functionality of RasMol to be enable. This enables   
                         other software to connect to a running RasMol. This  
                         should be undefined on machines not supporting       
                         BSD-style TCP/IP sockets (such as VMS).              
            APPLEMAC     This determines whether the program is to run on an  
                         Apple Macintosh or PowerMac. By default, this option 
                         is disabled. The Macintosh code may be compiled to   
                         be either EIGHTTBIT or THIRTYTWOBIT and will         
                         generate images effectively.                         
            IBMPC        This determines whether the program is intended to   
                         run on an IBM PC or compatible. By default, this     
                         option is disabled.                                  
            MSWIN        This determines whether the program is intended to   
                         run on an IBM PC or compatible under MS Windows. By  
                         default, this option is disabled.                    
            PROFILE      Defining PROFILE enables code to profile RasMol      
                         execution.                                           
            XPROCARCH    Defining XPROCARCH enables code for raswin that gets 
                         detailed information about the operating system and  
                         processor                                            
            USE_UNAME    Defining USE_UNAME enables code for rasmol under X11 
                         that gets detailed information about the operating   
                         system and processor.                                
            USE_CBFLIB   Defining USE_CBFLIB enables code t that depends on   
                         CBFLIB for map reading and writing.                  

            To summarise;

     A typical UNIX build:
          /* #define IBMPC        */
          /* #define MSWIN        */
          /* #define APPLEMAC     */
          #define X11WIN
          #define UNIX

          /* #define DIALBOX      */
          #define SOCKETS
          #define TERMIOS
          #define PROFILE
          #define MITSHM
          #define USE_UNAME
          #define USE_CBFLIB

     A typical Windows build:
         #define IBMPC
         #define MSWIN
         /* #define APPLEMAC      */
         /* #define X11WIN        */
         /* #define UNIX          */

         /* #define DIALBOX       */
         /* #define SOCKETS       */
         #define TERMIOS
         #define PROFILE
         #define MITSHM
         #define USE_CBFLIB

     A typical Macintosh classic build:
         /* #define IBMPC         */
         /* #define MSWIN         */
         #define APPLEMAC
         /* #define X11WIN        */
         /* #define UNIX          */

         /* #define DIALBOX       */
         #define SOCKETS
         #define TERMIOS
         #define PROFILE
         #define MITSHM
         /* #define USE_CBFLIB    */


            Any comments, suggestions or questions about this modified
            version should be directed to Herbert J. Bernstein at
            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 Help File |
      | Donate to Support RasMol | Release README | Register your RasMol |

     ----------------------------------------------------------------------

            Updated 19 July 2009.
            Herbert J. Bernstein
            Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
            yaya@bernstein-plus-sons.com
