The following operating systems are presently supported:
VIEWMOL 2.1 has been written 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 program. It can be found on
many ftp sites, e. g. at sgi.com under
graphics/tiff/tiff-v3.4-tar.gz.
Most Linux distributions already include this library. 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 libGLw.a. This library is provided with Mesa (in the directory
widgets-sgi), but has to be compiled separately (e. g. on Linux with
make linux-elf
). Alternatively, the library libMesaGLw.a in
widgets-mesa can be used (has also to be compiled separately), but the
getmachine
script has to be modified for this since the name of
this library is different.
Linux users need Motif to compile and run the program (if the program
complains about
"viewmol: can't load library 'libXm.so.2'
" Motif is missing). The
freeware Motif clone Lesstif (http://www.lesstif.org/)
can be used with Viewmol starting with version
0.81. There are, however, some glitches with Lesstif (e. g. shortcuts don't
work). For those people who do not have Motif on Linux a precompiled binary
which has been statically linked to the Motif library has been made available.
Linux users also have to have Mesa installed on their system to use
VIEWMOL. The Linux versions have been
statically linked with libGLw.a since not all Linux distributions provide
this library.
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. It is possible to use the library provided with Mesa in widgets-sgi
instead of installing above mentioned subsystem.
Installation of the program is simple. VIEWMOL comes as gzipped tar
file, viewmol.source-x.y.z.tgz
. Unzip and untar it using
gunzip viewmol.source-x.y.z.tgz
and tar -xvf viewmol.source-x.y.z.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
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
(vide infra) and the installation is
complete. Otherwise you have to recompile the program. The program 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 program 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
LDFLAGS
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 compilers 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 program 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 program 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 program 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 programs 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 program are installed and can be found in your path you do not need to set these resources. If these program 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 program 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 programs which use
command line arguments