RasMol 2.6
              Molecular Graphics Visualisation tool.

                           Roger Sayle 
                  Biomolecular Structures Group
              Glaxo Wellcome Research & Development
                  Stevenage, Hertfordshire, UK.
                           October 1996


    This file explains how to transfer, compile and install RasMol v2.6 on
your system. This version of the RasMol Molecular graphics package will 
run on UNIX, VMS, Macintosh and Microsoft Windows (OS/2 and Windows NT). 

[1] Obtaining RasMol v2.6
=========================

The current version of RasMol may be obtained by anonymous FTP from 
either ftp.dcs.ed.ac.uk in the directory /pub/rasmol or from 
src.doc.ic.ac.uk in the directory /packages/rasmol. These sites are
also mirrored at several other locations around the world. RasMol may
also be obtained by electronic mail by sending the message "help software"
to "netserv@embl-heidelberg.de". Follow the instructions provided by
EMBL for unpacking the software from the e-mail messages.

To transfer by anonymous ftp, type "ftp ftp.dcs.ed.ac.uk" 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 pub/rasmol" to change
the directory to /pub/rasmol and then type "binary" to avoid corrupting
the files during the transfer. For each file you wish to transfer, type
"get " 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.

The problem with rasmac.sit.hqx being reported as a corrupt StuffIt/BinHex 
archive is caused by FTP the end-of-line characters between UNIX and 
Macintosh platforms. 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.
Apparently using StuffIt or StuffIt Lite will not work directly. First use
BinHex to unhex the file rasmac.sit and then use StuffIt to extract and
uncompress the source files and executable. When using BinHex please 
make sure the "TEXT filter" option on the File Menu is disabled.
Alternatively, if you are transfering via a local UNIX machine, use the
command, `tr "\015" "\012" < rasmac.sit.hqx > temp.sit.hqx' to translate
all the carriage returns to linefeeds thus avoiding the problem.

Depending upon the type of machine, you'll need to transfer one or more 
of the following files:

	RasMol2.tar.Z	UNIX 'tar'ed 'compress'ed archive containing the
                        complete source code and documentation of the
                        RasMol molecular graphics package.

	RasMol2.tar.gz  UNIX 'tar'ed 'gzip'ed archive containing the 
                        complete source code and documentation of the
                        RasMol molecular graphics package.

        rasmac.sit.hqx  Apple Macintosh 'BinHex' and 'StuffIt' archive
                        of the RasMol source code including a 'fat'
                        binary for both Macintosh and PowerMac.

        raswin.zip      MS-DOS PkZip archive of the MS Windows version
                        of the RasMol source code including a binary
                        for MS Windows v3.1.

        rasmenu.zip     MS-DOS PkZip archive of the Visual Basic Graphical
                        User Interface to RasMol including executable.


To unpack the file RasMol2.tar.Z on a UNIX machine type the command
"uncompress RasMol2.tar.Z" and then the command "tar -xvf RasMol2.tar"
to extract the files in a subdirectory under the current directory.
Once the files have been sucessfully extract, you can delete the
file RasMol2.tar with the command "rm RasMol2.tar".

To unpack the file RasMol2.tar.gz on a UNIX machine, type "gunzip
RasMol2.tar.gz" to use GNU gunzip to uncompress the files. Then
follow the instructions above.

To unpack the file rasmac.sit.hqx, start up the application "StuffIt 
Expander" and select the option "Exapnd" from the "File" menu. This
should create the folder "RasMol2". You can then delete the files
"rasmac.sit.hqx" and "rasmac.sit" by dragging their file icon and
dropping them on the "trash can".

To unpack the files raswin.zip and rasmenu.zip, type the command
"pkunzip -d raswin.zip" and "pkunzip -d rasmenu.zip". You must have
version 2.04 or later of PKUNZIP.EXE


[2] Installing RasMol v2.6
==========================

UNIX X11:
---------
[1] Type the command "xmkmf" to generate a "Makefile" for your particular 
    system from the distributed Imakefile 

    Alternatively (or if the first method fails), copy the file Makefile.in
    to Makefile, using the command "cp Makefile.in Makefile", then modify 
    the contents of the Makefile to determine your local C compiler,
    compiler and linker options. The default set up is for an 8bit UNIX
    workstation with the X11 shared memory extension, compiled using the
    GNU C Compiler. Changing the line "CC=gcc" to "CC=cc" will use the
    machines native compiler but will require changing "CFLAGS" for your
    platform.

    RasMol may be built for E&S workstations using the command "make esv".

    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.

[2] Modify the #defines in the file rasmol.h (see below)
        Note: IBMPC should not be defined.
[3] Compile the program using the UNIX make utility. (i.e. type "make")
[4] Place the 'rasmol' executable on the execution PATH, i.e. /usr/local/bin
[5] Install rasmol.hlp as /usr/local/lib/rasmol/rasmol.hlp (or at a loctaion
    indicated by the environment variable RASMOLPATH).
[6] If you have the UNIX utilities "uncompress" or "gunzip" ensure they are
    on the user's default PATH.
[7] Set the environment variable RASMOLPDBPATH to the directory containing
    the Broohaven PDB database, if one exits.
[8] Place any system wide initialisation parameters into the file "rasmolrc"
    in the directory pointed to by RASMOLPATH.
[9] It is possible to set-up RASMOLPATH and RASMOLPDBPATH each time the 
    program is running by renaming rasmol to rasmol.exe, and using a script
    similar to the one in "rasmol.sh" of the standard distribution.
[10] If appropriate place "rasmol.1" or "rasmol.0" in the appropriate place
     for UNIX man pages, and optionally place "rasmol.html" somewhere in 
     your WWW hierarchy (if available at your site).


MS Windows v3.1:
----------------
[1] Copy both the executable RASWIN.EXE, RASMOL.HLP and RASWIN.HLP to an
    appropriate directory.
[2] Install the program in MS Windows using the New option of the Program
    Manager's File Menu. Set the Description of the Program to "RasWin v2.6"
    and the Current Directory, to the directory containing the files.
[3] Install the RasMol Help file using the New option of the Program
    Manager's File Menu. Set the Description to "RasWin Manual", the
    command to "C:\WINDOWS\WINHELP RASWIN.HLP" and the working directory
    to the appropriate directory.

MS Windows NT v3.x and Windows 3.1x with Win32S:
-----------------------------------------------
[1] Copy both the executable RASWIN32.EXE, RASMOL.HLP and RASWIN.HLP to an
    appropriate directory.
[2] Install the program in MS Windows using the New option of the Program
    Manager's File Menu. Set the Description of the Program to "RasWin32 v2.6"
    and the Current Directory, to the directory containing the files.
[3] Install the RasMol Help file using the New option of the Program
    Manager's File Menu. Set the Description to "RasWin Manual", the
    command to "C:\WINDOWS\WINHELP RASWIN.HLP" and the working directory
    to the appropriate directory.

MS Windows NT v4.x and Windows 95
---------------------------------
[1] Copy both the executable RASWIN32.EXE, RASMOL.HLP and RASWIN.HLP to an
    appropriate directory.
[2] Create a shortcut icon to RasWin on the Desktop or in a folder.
[3] Select the RasWin icon then simultaneously press ALT-ENTER (or right
    click on the icon and select "Properties" from the menu).
[4] Select the "Shortcut" tab in the Properties dialog box.
[5] At the "Start In:" prompt, type in the path of the appropriate working
    directory.


Macintosh and PowerMac
-----------------------
[1]  Place both "RasMac v2.6" and "rasmol.hlp" in the same Macintosh folder

VAX/VMS
-------
[1] Modify the #defines in the file rasmol.h (see below)
        Note: IBMPC, MITSHM and TERMIOS should not be defined.
[2] Copy all the files from the "vms" directory to the source directory.
[2] If your VAX site has an MMS license type the command "MMS",
    otherwise use the DCL build script by typing "@build.com"
[3] The program may be run by typing "RUN RASMOL.EXE", the X Windows
    server is specified by a VMS command of the form:
	SET DISPLAY/CREATE/TRANSPORT=TCPIP/NODE=
[4] The symbol should be defined the the path of RASMOL.EXE using :==
[5] The file rasmol.vms contains a ascii VMS help file that can
    be compiled in to the VMS on-line help system.


[3] Recompiling RasMol v2.6
===========================

MS Windows v3.1:
----------------
[1] Use Makefile.pc instead of Makefile, by copying it to MAKEFILE.
[2] Modify the contents of the Makefile to determine your local C compiler,
    compiler and linker options. 
[3] Modify the #defines in the file rasmol.h (see below)
        Note: EIGHTBIT and IBMPC should all be defined
              APPLEMAC, DIALBOX, MITSHM and TERMIOS should not be defined.
[4] Compile the program using the Microsoft Optimizing C Compiler Version
    7's (or Microsoft Visual C++'s) NMAKE program under MS-DOS.

MS Windows NT
-------------
[1] Using Microsoft Visual C++, create a new project adding all the
    "*.c" source files except "rasmol.c", "x11win.c", "rasmac.c" and
    "applemac.c". Add the Windows resource source file "raswin.rc".
    or alternatively use Makefile.nt by copying it to MAKEFILE.
[2] Follow the instructions from [2] onwards as for MS Windows v3.1.

Apple Macintosh and PowerMac
----------------------------
[1] Create a project in either the Symmantec C/C++, Think C or Metrowerks 
    C compiler environments and add all the C source files ("*.c") to 
    the project. On 68k development systems all C files should be placed
    in separate segments [however rasmac.c and applemac.c can share a
    segment and abstree.c and command.c can share a segment].
[2] Add the "rasmac.rsrc" resource file to the project.
[3] For the Symantec/Think C environment add the "ANSI" or "ANSI-small"
    library from "Standard Libraries" folder and the "MacTraps" library
    from the "Mac Libraries" folder. The choice of "ANSI" or "ANSI-small"
    is dependent upon the size of integer by the compiler. See dialog
    'Edit'->'Options'->'Think C..'->'Compiler Settings'.  2-byte integers 
    require "ANSI-small" and 4-byte integers require "ANSI".
[4] For the Metrowerks 68K Compiler add the libraries "MacOS.lib" and
    "ANSI (2i) C.68K.Lib" to the project. [Note: If compiling for 4byte 
    integer size and/or 68881 maths instructions select the approriate 
    ANSI C Library].
[5] For the Metrowerks PPC Compiler add the libraries "MWCRuntime.Lib",
    "InterfaceLib", "MathLib" and "ANSI C.PPC.Lib". This should work
    fine for Metrowerks C++ v1.1.  Apparently, Metrowerks C++ v1.2 also
    requires "console.stubs.c". [Thanks to Graham Palmer]
[6] In Metrowerk's "Edit" "Preferences" "Project" or Symmantec's "Project"
    "Set Project Type", set the project type to Application (Type 'APPL'), 
    Creator 'RSML', and the SIZE flags to include "is32bitCompatible", 
    "isHighLevelEventAware", "localAndRemoteHLEvents".
[7] Modify the #defines in the file "rasmol.h" (see below).
        Note: APPLEMAC should all be defined
              IBMPC, DIALBOX, MITSHM and TERMIOS should not be defined.
[8] Compile RasMol using the "Build Application..." Menu Item.
[9] To create a `fat' binary, use Apple's ResEdit to copy and paste the
    CODE, DATA and XREF resources from the Metrowerks 68K executable 
    into the resource fork of the Metrowerks PPC executable.
[10] The Installed Application's name should be "RasMac v2.6"


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
SIXTEENBIT
EIGHTBIT	This determines whether RasMol will display and produce
		8bit, 16bit or 32(24) bit output. By default the symbol 
                EIGHTBIT is 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 under MS Windows. By default, this 
                option is disabled. If this option is defined the options 
                EIGHTBIT and INVERT must be defined, and TERMIOS undefined.

To summarise;
    A typical UNIX build:
        /* define IBMPC    */
        /* define APPLEMAC */
        /* define DIALBOX  */
        #define TERMIOS
        #define MITSHM
        #define EIGHTBIT

    A typical Windows build:
        #define IBMPC
        /* define APPLEMAC */
        /* define DIALBOX  */
        /* define TERMIOS  */
        /* define MITSHM   */
        #define EIGHTBIT

    A typical Macintosh build:
        /* define IBMPC    */
        #define APPLEMAC
        /* define APPLEMAC */
        /* define DIALBOX  */
        /* define TERMIOS  */
        /* define MITSHM   */
        #define EIGHTBIT
        
    A typical VMS build:
        /* define IBMPC    */
        /* define APPLEMAC */
        /* define DIALBOX  */
        /* define TERMIOS  */
        /* define MITSHM   */
        #define EIGHTBIT

Roger
-- 
Roger Sayle                                INTERNET:  ras32425@ggr.co.uk
Glaxo Wellcome Medicines Research Centre,             rasmol@ggr.co.uk
Gunnels Wood Road, Stevenage,        Tel:   +44 (0)1438 763246 (direct line)
Hertfordshire, SG1 2NY, U.K.         Fax:   +44 (0)1438 763082