The following operating systems are presently supported:
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:
OPT
-O6 -mpentium
, requires Pentium
aware gcc; -O2
else).CFLAGS
INCLUDE
LIBRARY
LIBS
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 .
VIEWMOL uses by default English as language, but it has been written so that other
languages can easily be used . 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 %sIf 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 arguments