Ribbons Source Code
Installation
A basic familiarity with UNIX and system administration is assumed.
Everything has been set up for the C-shell.
It is assumed you have all the source code directories from over the net.
Important Note: Please read the file 'Read.Me' in the ~ribbons/install
directory, which is probably more up-to-date than this page.
Compilation
As distributed, the `ribbons' software suite should be ready to run
on any SGI system. There may also be a ready-to-run version available
for other systems - check it out on the web site.
Else, you will need to recompile by executing the commands in this directory:
- configure
to set appropriate Makefiles for the target machine.
You will be prompted for one of the supported machine types.
- make clobber
to get rid of all old compiled files, libraries, and executables.
- make compile
to compile all the files, libraries, and executables.
You will be prompted for the name of your C++ compiler.
Each directory will be entered in turn and its unix Makefile invoked.
First, please see the special notes below for Alpha and Linux boxes.
There may be some warnings. Please report any errors to me!
- make install
to move all the executables to the $RIBBONS_HOME/bin directory.
Your `path' should include $RIBBONS_HOME/bin to run all the programs.
- Make clean
to get rid of all the old compiled files.
No need to do this with an SGI, the distribution is already `clean'.
Do this once the program has been tested (see below).
Special notes for Compaq (DEC) Alpha machines
The widgets connecting X/GL are in a different place than on the SGI.
Suggest you make symbolic links of the small *.h files,
(else change LOTS of includes, or hack on the Makefiles).
You need root permission to do this:
cd /usr/include/GL
ln -s /usr/include/X11/GLw/GLwMDrawA.h .
ln -s /usr/include/X11/GLw/GLwDrawA.h .
You must have the TIFF libraries installed if you want to save images.
TIFF and other libraries are available from:
http://www.tru64unix.compaq.com/demos/ossc-v5.0/html/shwindex.htm
or you can get them from my compilation, tiff 3.4, version 5.1 alpha.
You need:
/usr/lib/libtiff.a
/usr/include/tiff.h, tiffio.h, etc
Special notes for Linux boxes
These boxes require currently too much care and feeding for my taste.
Have relied on the kindness of strangers (especially Suhaib Siddiqi
of Inspire Pharmaceuticals) to get this going.
The problem is getting the right X/Motif/OpenGL libraries in place.
I hope more kind strangers will provide me with working Makefiles
and/or libraries for their particular setup.
Currently, two setups are supported:
linux == just like on my box, with these libs loaded:
-lXm -lGLw -lGLU -lGL -ltiff -lX11 -lXt -lXext -lXp -lm
mesa == just like on David Johnson's box, with these libs:
-L/usr/X11R6/lib -lMesaGLw -lXm -lXt -lGLU -lGL -lX11 -lXext -lXp -ltiff -lm
Program testing
To test the `ribbons' distribution, after recompiling if necessary,
and setting your command path:
First, as a normal user, create a new directory and go there, eg:
mkdir ribtest
cd ribtest
Then execute the perl script test protocol interactively:
ribbons-test
This runs over 40 representative commands with various options,
and compares their output to that in $RIBBONS_HOME/test.
A summary is output to the terminal, and a complete record
is saved to the file `ribbons-test.log'
Several `differences' will appear, just due to temporary file names.
Please report any non-trivial errors to me!
carson@uab.edu
Program organization
The default distribution consists of the main ``$RIBBONS_HOME''
directory and the following subdirectories:
- analysis
Structure analysis tools.
- bin
Executable versions of the programs (some are simply
shell scripts; most are links to executable commands).
- data
Assorted example data.
All files referred to in the manual are found here.
- gallery
Artistic images (optional) in *.rgb format.
- help
The hypertext help screens and *.gif images.
- images
Artistic images (optional) in *.gif format.
- misc
Assorted trivia.
- rgb
Sample images (optional) in *.rgb format from example data.
The source code distribution consists of Makefiles, C++ ( *.C )
source code (and some FORTRAN), and *.h include files
in the following subdirectories:
- analysrc
Source code for structure analysis tools.
- elmo
Tcl/Tk data preparation GUI programs.
- facets
Density map surface faceting programs.
- fithx
Helix fitting program suite source code.
- gutils
Assorted graphics utilities
- install
The Make.* shell scripts to install and compile all programs.
- ms
Molecular surface source code (old version).
- msp
Molecular Surface Package conversion utilities.
- nutils
Newer utilities that use OOP library.
- oop
First-pass OOP code for the 'ribbons++' project
- ps
PostScript utilities source code.
- src
Main ribbons graphics program.
- utils
Most data preparation utility programs and libraries for ribbons .
Changing things
If you are feeling lucky, dig right in.
If you have a support license, I'll be happy to advise
and might even help.
Theory
See