3 Installation

VIEWMOL 2.4 was developed on an Athlon PC with an Nvidia graphics card running Red Hat Linux 9. Hardware acceleration for 3D is not strictly necessary, but recommended. VIEWMOL also works with Brian Paul's OpenGL compatible library Mesa. VIEWMOL has been ported to PCs with FreeBSD, Silicon Graphics computers, IBM RS/6000, DEC Alpha, Suns, Hewlett Packard 9000/735, Macintoshs with MacOS X, and Windows PCs using the Cygwin tools. Since Mesa runs on any machine which has the X Window System it should be possible to run VIEWMOL on any machine which supports the X Window System. However, for best performance a native OpenGL implementation is recommended.

Binaries are presently supported on the following operating systems:

PC: Linux 2.4.x, FreeBSD 5.1
Macintosh: MacOS X (courtesy of Gert von Helden, helden@fhi-berlin.mpg.de)

On these operating systems the program was tested. Others may also work, but this is not certified. Previous versions of VIEWMOL have also been tested on the following systems:

DEC Alpha: OSF1 V4.0 (tested only with Mesa; courtesy of Pablo Vitoria Garcia, qibvigap@lg.ehu.es)
IBM: AIX 4.1
HP: HP-UX 9.5 (tested only with Mesa),
SGI: Irix 6.3
Sun: SunOS (courtesy of Keith Refson, Keith.Refson@earth.ox.ac.uk)
PC: Microsoft Windows using Cygwin (courtesy of Noda Tomoyuki, noda.tomoyuki@canon.co.jp)

but since the author does not have access to any of these systems testing of newer versions was not possible. It can, however, be assumed that VIEWMOL will at least compile on these systems.

VIEWMOL 2.4 is provided precompiled for a number of architectures. Precompiled binaries are packaged separately from source, documentation, and examples:

x86 Linux viewmol-2.4.bin.Linux.tgz
x86 FreeBSD viewmol-2.4.bin.FreeBSD.tgz
Macintosh viewmol-2.4.bin.MacOSX.tgz

VIEWMOL can be downloaded from:

SourceForge
http://viewmol.sourceforge.net/

Before installing VIEWMOL you need to make sure that the following software/libraries are available:

OpenGL or Mesa (libGL.so, libGLU.so or libMesaGL.so, libMesaGLU.so)
This is probably only relevant for installations on Linux. Most Linux distributions now include support for OpenGL programs. Mesa can be found at http://sourceforge.net/projects/mesa3d.
X Window System
This is only relevant for installations on Microsoft Windows and Macintoshs. For Microsoft Windows Cygwin needs to be installed which includes the X Window System http://www.cygwin.com/. Apple distributes the X Window System for Mac OS X at http://www.apple.com/macosx/.
Motif or Lesstif (libXm.so)
This is probably only relevant for installations on Linux, Microsoft Windows, and Macintoshs. Motif can be found at http://www.motifzone.org/download/. Lesstif can be found at http://www.lesstif.org/. For Microsoft Windows Cygwin includes Lesstif. For Mac OS X the Fink distribution http://fink.sourceforge.net/ includes Lesstif.
Python >=2.2
Linux distributions usually include Python. For other systems you need to obtain Python from http://www.python.org/
TIFF library (libtiff.so)
Linux distributions include this library. On Silicon Graphics this library is installed if the ifl_eoe and ifl_dev packages have been installed. For other systems you need to obtain and compile this library (e. g. from ftp://ftp.remotesensing.org/pub/libtiff)
PNG library (libpng.so)
Linux distributions include this library. For other systems you need to obtain and compile this library (from Sourceforge under http://libpng.sourceforge.net/)

Installation of the program is simple. VIEWMOL comes as gzipped tar file, viewmol-2.4.src.tgz. Unzip and untar it using gunzip viewmol-2.4.src.tgz and tar -xvf viewmol-2.4.src.tar. You get six subdirectories, source, doc, scripts, tests, locale, and examples, and the configuration file viewmolrc. Copy all files you got into an arbitrary directory. If you want to install precompiled binaries, download the appropriate file for your operating system and unpack it from the same directory you unpacked the source code. This will create a subdirectory in the source directory which holds the binaries (the name of this directory starts with the name of your operating system as you get it from uname -s and may contain a CPU specific ending). If you run the supported operating systems you have to set the environment variable $VIEWMOLPATH to point to the directory where you unpacked VIEWMOL (the compiled-in default for VIEWMOLPATH is /usr/local/lib/viewmol) and the installation is complete. Otherwise you have to recompile the program (cf. p. ). The program uses dynamical memory allocation so that every size of a molecule can be handled which fits the hardware limits of your computer.

The installation directory also contains a file viewmolrc. You might have a look into this file and adapt it to your needs. The format is described at page . In general the defaults should work fine.

VIEWMOL uses by default English as language, but it has been written so that other languages can easily be used¹. The distribution contains localized versions of all the program messages, menus, dialog boxes etc. in the directory locale (currently for English, French, German, Hungarian, Polish, Russian, and Spanish). If you want to use a different language for a system wide installation, copy the corresponding Viewmol file to your applications default directory (usually /usr/lib/X11/app-defaults). If you want to use a different language only for some users, instruct them to configure the language through VIEWMOL's Configuration menu. VIEWMOL will run without any of the localized files installed. So if you are happy with English and want to change only a few settings you do not need to install any of the files from the locale directory.

VIEWMOL needs a few external programs for some of its functions. Once you have installed VIEWMOL and set VIEWMOLPATH, you can start VIEWMOL, press Cancel in the file selection box which will appear, and press the right mouse button in the blue VIEWMOL window. A popup menu will appear where the last but one option is Configuration .... Choosing this option displays a dialog where you can set path names to four external programs. These are (including their defaults)²:

Location of Web browser:                    mozilla %s
Location of Moloch:                         moloch
Location of Rayshade:                       x-povray +I%s +O%s +W%d +H%d
Location of display program for images:     xv %s

If these program are installed and can be found in your path VIEWMOL will automatically display the correct path names in the dialog. The %s and %d are placeholders for the file name and dimensions and are required for programs which use command line arguments. Once you have set these path names, choose Save from the buttons in the dialog and these settings will be stored permanently in $HOME/.Xdefaults.

The correct installation of VIEWMOL can be tested through the included test scripts (cf. p. ).

Footnotes

... used ¹: This manual assumes that the English version of VIEWMOL is used. The shortcuts for other languages are different, but obvious in the menus.
... defaults)²: Moloch may be called TurboPROP if you got TURBOMOLE from Accelrys Inc.

Jörg-Rüdiger Hill Fri Oct 31 14:19:21 CET 2003