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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
|
