next up previous
Next: Synopsis Up: Viewmol Manual Previous: Copyright

Installation

  VIEWMOL 2.0 was developed on a Pentium notebook running Linux using Brian Paul's OpenGL compatible library Mesa. It also compiles with OpenGLTM without any problems. VIEWMOL has been ported to Silicon Graphics computers, IBM RS/6000, DEC Alpha, and Hewlett Packard 9000/735. Since Mesa runs on any machine which has X windows it should be possible to run VIEWMOL on any machine which supports X windows. However, for best performance a native OpenGL implementation is recommended. VIEWMOL does not run on Windows PC or Macs. For use on PCs or PowerMacs Linux is required and highly recommended.

The following operating systems are presently supported:

(On these operating systems the programme was tested. Others may also work, but this is not certified.)

VIEWMOL 2.0 has been completely rewritten in C. For recompilation of VIEWMOL you need a C compiler. TIFF files are supported by the freely available TIFF library which is also necessary to compile the programme. It can be found on many ftp sites, e. g. at sgi.com under graphics/tiff/tiff-v3.4-tar.gz. If you want to link VIEWMOL with Mesa instead of with OpenGL you will need Mesa (http://www.ssec.wisc.edu/~brianp/Mesa.html). Mesa includes support for OpenGL widgets under X windows with an additional library libMesaGLw.a. This library is provided with Mesa (in the directory widgets-old), but has to be compiled separately (./configure --with-motif; make). Alternatively, the library in widgets-sgi can be used (has also to be compiled separately), but the getmachine script has to be modified for this. Linux users need Motif to compile and run the programme (if the programme complains about "viewmol: can't load library 'libXm.so.2'" Motif is missing). The released precompiled binary has been dynamically linked to the Motif libraries. There seem to be problems with the compilation on SGI's. Make sure you have the gl_dev.sw.widget subsystem installed which includes the OpenGL widgets for Motif. If during the compilation the compiler complains about "Cannot open file GL/GLwMDrawA.h for #include" this package is missing.

Installation of the programme is simple. VIEWMOL comes as gzipped tar file, viewmol.tgz. Unzip and untar it using gunzip viewmol.tgz and tar -xvf viewmol.tar. You get three subdirectories source, man, and examples, three resource files (English, German, Russian) Xdefaults.* and the configuration file viewmolrc. Copy all files you got into an arbitrary directory. If you run the supported operating systems you have to set the environment variable $VIEWMOLPATH (vide infra) and the installation is complete. Precompiled binaries can be found in subdirectories of the source directory (the names of these directories start with the name of your operating system as you get it from uname -s and may contain a CPU specific ending). Otherwise you have to recompile the programme. The programme uses dynamical memory allocation so that every size of a molecule can be handled which fits the hardware limits of your workstation.

If you want to recompile the programme and you are running one of the supported operating systems (this may be necessary on IBM workstations since the formats of the executables are not compatible between different releases of AIX - don't worry, IBM didn't) you may type make (this tries to build VIEWMOL using OpenGL on all operating systems except on Linux, to build using Mesa type make viewmol_mesa; make tm bio readgauss). The shell script getmachine determines the operating system you are running and sets some options for the compiler. If this does not work you should have a look into the Makefile. The options set are explained there. That are the following:

The getmachine shell script will ask you for the path names to the TIFF library and to the include files necessary with this library. If you compile with Mesa the script will also ask you for the location of the Mesa libraries and include files. You may specify these path names using environment variables if you put the name of the variable in parentheses (e. g. $(HOME)). These path names are assigned to the LIBTIFF, TIFFINCLUDE, MESALIB, and MESAINCLUDE flags and stored in a file .config.<OS> where <OS> is the output of the uname -s command on your machine. If this file already exists, getmachine does not ask for these path names.

Silicon Graphics compiler on 64-bit operating systems (IRIX64 - R8000, R10000) will produce a lot of warning messages concerning casts of pointers to integers. These can be safely ignored.

The make procedure will build the programme in a directory whose name depends on the operating system and type of CPU you are using. You will find all executables in this directory. After building the programme it can be used. You have to set the environment variable VIEWMOLPATH to the directory which contains your system wide viewmolrc file (normally the installation directory of VIEWMOL). You might have a look into this file in the installation directory and adapt it to your needs. The format is described at page gif.

VIEWMOL uses by default English as language, but it has been written so that other languages can easily be used gif. The distribution contains files Xdefaults.<language> which contain all the programme messages, menus, dialog boxes etc. in other languages (currently German and Russian). If you want to use a different language for a system wide installation, copy the corresponding Xdefaults.<language> file to your applications default directory (usually /usr/lib/X11/app-defaults) and rename it to Viewmol. If you want to use a different language only for some users, instruct them to put the contents of Xdefaults.<language> into their $HOME/.Xdefaults files. VIEWMOL will run without any of the Xdefaults.<language> files installed. So if you are happy with English and want to change only a few settings it is sufficient to put only the changed resources into your $HOME/.Xdefaults.<language> file.

There are a few resources you might want to set since they specify the location of other programmes used by VIEWMOL. These resources and their defaults are the following:  

Viewmol.webBrowser:                 netscape %s
Viewmol.Moloch:                     moloch
Viewmol.Rayshade:                   rayshade
Viewmol.DisplayRLE:                 xv %s
If these programmes are installed and can be found in your path you do not need to set these resources. If these programmes are not in your path you have to specify the full path and the name of the executable in the corresponding resource. If you want to use another programme to display RLE files you also have to specify it in the Viewmol.DisplayRLE resource. The %s is a placeholder for the file name and is required for programmes which use command line argumentsgif.


next up previous
Next: Synopsis Up: Viewmol Manual Previous: Copyright

Jörg-Rüdiger Hill
Sun Dec 8 14:15:58 PST 1996