                           Installation Instructions
                                 RasMol 2.7.4.1

                     Molecular Graphics Visualisation Tool
                                26 January 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 (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 2.7.3 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

+-----------------------------------------------------------------------------+
| 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 1998-2008

   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 26 January 2008
            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, 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 v2.7.4.1

   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 2.7.4 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_2.7.4.1.tar.gz

   or on the web at:

   http://www.bernstein-plus-sons.com/software/RasMol_2.7.4.1.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 2.7.4.1 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.

   In addition, depending on what has already been installed on your system,
   you may need one or more external packages. 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://blondie.dowling.edu/projects/rasmol. These kits are snapshots of
   the versions in use at the time of the build of RasMol 2.7.4. 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.

   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 v2.7.4

    UNIX X11:

   If you are using a precompiled binary, see the instructions that are
   provided with the binary kit.
    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. Recommendations on Japanese shift-jis and Chinese
       GB2312 fonts are still being discussed. Suggestions would be
       appreciated.
    2. CBFlib: if you plan to read or write maps, you will need CBFlib. A
       copy of CBFlib 0.7.9 is included in external packages. You will need
       to make CBFlib.a.
    3. In the RasMol src directory, either
          * edit Imakefile to select the desired pixel bit depth; and
          * execute
             &npsp;xmkmf
            and
          * execite
             &npsp;make rasmol
       or
          * edit the script build_all.sh
          * excute build_all.sh
       to build as many variants of rasmol as possible.
    4. 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.
    5. 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.
    6. Modify the #defines in the file rasmol.h (see below) Note: IBMPC
       should not be defined.
    7. Edit the script rasmol_install.sh
    8. Execute rasmol_install.sh

    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.

   If you are building from source, you will need CodeWarrior version 9 to
   build both CBFlib and RasMol. Appropriate CodeWarrior project exports are
   provided as xml files.

    Macintosh under OSX:

   Follow the instructions for unix and run under the X11 system.

  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.

   THIRTYTWOBIT This determines whether RasMol will display and produce 8bit, 
   SIXTEENBIT   16bit or 32(24) bit output. By default the symbol EIGHTBIT is 
   EIGHTBIT     defined producing images with 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 26 January 2008.
   Herbert J. Bernstein
   Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
   yaya@bernstein-plus-sons.com
