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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
| 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. Darakevand L. Andrews (via the neartree package). Work on RasMol 2.7.5supported in part by grant 1R15GM078077-01 from the National Instituteof General Medical Sciences (NIGMS), U.S. National Institutes of Healthand by grant ER63601-1021466-0009501 from the Office of Biological &Environmental Research (BER), Office of Science, U. S. Department ofEnergy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH andgrant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporateschanges by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Workon RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281and EF-0312612 from the U.S. National Science Foundation and grantDE-FG02-03ER63601 from BER/DOE. The content is solely the responsibilityof the authors and does not necessarily represent the official views ofthe funding organizations.
The code for use of RasMol under GTK in RasMol 2.7.4.2 was written byTeemu 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 |
Herbert J. Bernstein,Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
yaya@bernstein-plus-sons.com
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 forversion 2.6.4 as the primary source. Changes were made inAugust 2000 for RasMol version 2.7.2, January 2001 for RasMolversion 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 andFebruary 2005 for RasMol version 2.7.3.
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of José Miguel FernándezFernández (Departamento de Bioquímica y Biología Molecular. Universidad de Granada.España (jmfernan@ugr.es)) a translation of theManual for Rasmol version 2.7.1 into Spanish is now available.La traducción española del manual de laversión de la Dra. Wong revisada por Eric Martz fue realizada porIsabel Serván Martínez y José Miguel FernándezFernández. La actual traducción del Manual de RasMol 2.7.1ha sido realizada usando como base la anterior de RasMol 2.6 por José Miguel Fernández Fernández.
Thanks to translations by Fernando Gabriel Ranea
THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******
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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 RasMolversion 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
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Please read the file NOTICE forimportant notices which apply to this package and forlicense 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 codeand user documentation of RasMol 2.7.5 may be obtained from http://blondie.dowling.edu/projects/rasmolandhttp://blondie.dowling.edu/projects/rasmol.andbyanonymous FTP at:
or on the web at:
Rasmol Program
As compiled version become available, they will be posted at http://blondie.dowling.edu/projects/rasmolandhttp://blondie.dowling.edu/projects/rasmol.
To transfer by anonymous ftp, type 'ftp ftp.bernstein-plus-sons.com' on the commandline. Several seconds later you'll be prompted for a username. Use theusername 'anonymous' and when asked for a password enter your e-mailaddress. Once logged in, type the command 'cd software/rasmol' to changethe directory to /software/rasmol and then type 'binary' to avoid corruptingthe 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 totransfer them in BINARY mode. The file sizes should be identical beforeand after the transfer.
NOTE: The Mac uses the 'carriage return' character to signify theend of a line, while UNIX machines use a 'linefeed'. If a file istransfered between these two machines in 'ASCII' mode all suchcharacters are exchanged, thereby corrupting the archive. Pleaseensure that you type the FTP command 'binary' before you transfer thefile, indicating that the file should be transfered withouttranslation.
If you wish to start from source code, you will need a RasMol source kit, andyou may need one or more external packages that are not part of RasMol, but whichare 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 'gunzipRasMol.tar.gz' and then the command 'tar -xvfRasMol.tar' to extract the files in a subdirectory under thecurrent directory.
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You will either need to have the following packages installed in your system, orto 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_LOCALhttp://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 partof RasMol and normally whould be obtained from their primary web sites, but,for convenience in installing RasMol, they have been gathered in theexternal_packages module in the CVS and as the External_Packages release on http://blondie.dowling.edu/projects/rasmolandhttp://www.sourceforge.net/projects/openrasmol.
These font kits are snapshots of the versions in use at the timeof the build of RasMol 2.7.5. The primary developer website for each package should be consulted for the latestversions. 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 srcdirectory.
For RasMol release 2.7.5 the package snapshots other than the font kits have been replaced by the tableof 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 eachsystem, 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 specifiedby the environment variable PATH) and copy rasmol.hlp to/usr/local/lib/rasmol/rasmol.hlp (or to the location indicated by theenvironment variable RASMOLPATH)
Installing RasMol v2.7.5
UNIX X11:
If you are using a precompiled binary, see the instructions that are providedwith the binary kit. In general, the binary kits for unix provided directlyby this project are tarballs of the $HOME/lib/RasMol_2_7_5 created byrunning the script in src/rasmol_install.sh. The MS windows kit isa NSIS installer to be double-clicked after downloading.
- Fonts: Followling the instructions for your system, install whateverX11 font packages you need to the language variants of RasMol you intend touse. 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 Japanesefonts in intlfonts-1.2.1.tar.gz in external_pakages seem to be satisfactory.
- In the RasMol src directory, either
Note for 64 bit CPUs: If you are building RasMol for a 64-bit CPUwith a compiler that has a 64-bit long data type, you must either usethe 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 Imakefilefrom 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
- Use the script rasmol_build_options.sh to build a new Imakefilefrom Imakefile_base. The valid options are:
- either
- execute
&npsp;xmkmf
and - execute
&npsp;make rasmol
- edit the script build_all.sh
- execute build_all.sh
- execute
- 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 comewith 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-editedversion 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 controlthe runtime behaviour of the program. The following directives may bedefined 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. |
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To summarise;
Any comments, suggestions or questions about thismodified version should be directed to Herbert J. Bernstein atrasmol@bernstein-plus-sons.com.
| 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 |
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
