README file for Sam 2.0.0

Sam is a program for predicting the structures of symmetrical protein complexes.
To install Sam, you will need to download and run the self-installer file using 
something like this:

   cd ~
   sh sam-2.0.0-x64.bin

This script will make a subfolder called "sam" and it will add any necessary 
environment variables to your start-up shell script. Normally, you will then 
be able to run the program from the command line by typing the command "sam" 
(without the quotes).

If you prefer to install the program manually, you should create a sam directory, 
and then uncompress the distribution files into it. For example, use something like:

   sh sam-2.0.0-x64.bin --noexec

   mv sam-dist-2.0.0/sam-2.0.0-x64.tgz /your-sam-directory

   cd /your-sam-directory

   zcat sam-2.0.0-x64.tgz  | tar xvpf -

You will then need to set some environment variables in your login file. Here are the 
main variables that you will probably need to set:

(for csh users, edit ~/.cshrc file)

   setenv SAM_ROOT      /your-login-or-top-level-folder/sam 

   setenv PATH           ${PATH}:${SAM_ROOT}/bin

(for bash users, edit ~/.bashrc)

   export SAM_ROOT=/home/dritchie/sam       <-  substitute the proper pathname here.

   export PATH=${PATH}:${SAM_ROOT}/bin

Here is a further environment variable you might wish to set

   SAM_RESULTS="./sam_results/"


The program is launched from a script called "sam" in the "sam/bin" directory.
If your PATH is correct, you should be able to test it using something like:

   cd sam/test
   
   sam -c2 d1bhga1.ent 

This will treat d1bhga1.ent as the source monomer, and Sam will make candidate complexes
with C2 symmetry.

Because Sam can generate several output files, it normally writes its output to a 
sub-directory called "./sam_results/". In fact, Sam makes a new sub-sub-folder for each 
query, so in this case you will get a folder called "sam/test/sam_results/d1bhga1":

   ls -1 sam/test/sam_results/d1bhga1

If you really do not want Sam to make sub-directories, use:

   sam -nosubdirs d1bhga1.ent 

This will put all the results files directly in to "./sam_results/". If you really 
do not want a results sub-folder, set the SAM_RESULTS variable:

    SAM_RESULTS=/tmp/junk

or

   SAM_RESULTS="."

For more options, please use

   sam -help


Happy sam-ing!


Dave Ritchie 
INRIA Nancy Grand Est
Nancy, France

email:     Dave.Ritchie AT inria.fr (please make your own AT sign)
web:       http://www.loria.fr/~ritchied/
Sam:       http://sam.loria.fr/