RasMol V2.7.5 INSTALL

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# Installation Instructions
RasMol 2.7.5

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### 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 © Roger Sayle 1992-1999

and Based on Mods by

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

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 Serván Martínez, José Miguel Fernández Fernández | 2.6 Manual | Spanish
José Miguel Fernández Fernández | 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, A. Davassi, M. Masullo, C. Liotto | 2.7.1 menus and messages 2.7.1 help file | Italian
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
Copyright © 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 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.

Thanks to translations by Fernando Gabriel Ranea in late 2000 and early 2001, RasMol is now capable of rendering most menu items and messages in Spanish. Jean-Pierre Demailly provided French translations of menus and messages in January 2001. Giuseppe Martini and Giovanni Paolella 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.

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. 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