Extract executables by typing "tar xvf psed1.0.tar"

'hieraln' and 'hierview' were compiled under a RedHat 5.9 Linux operating system 
(kernelrelease 2.6.18-371.1.2.el5) running on an Intel Xeon x86_64 machine.

Type ./hieraln or ./hierview for usage.

To create input for these programs you can use:
  1. the gismo (http://gismo.igs.umaryland.edu/) program to obtain an alignment in the cma format 
  2. the omcBPPS program (http://chain.umaryland.edu/omcbpps/) to obtain hierarchy files from the alignment.

The hieraln program adjusts each subgroup's alignment within the hierachy.  
The hierview program uses output from the hieraln program to create:
  1. pymol files for visualizing correlated residue patterns 
  2. contrast alignment files in rich text format (rtf).   

Currently running a PSED analysis is quite involved.  To simplify this process, 
the psed tarball also includes omcBPPS-generated files for N-acetyltransferases 
(i.e., natA.sets, natA.hpt, natA.mma), which are used as input to the hieraln program.  

The hieraln program creates the following output files as input to the hierview program:

   natA_himsa.sets, natA_himsa.tpl, natA_himsa.hpt, and natA_himsa.cma 

To create pymol output files using hierview: 
   1. uncompress and untar pdb_nat.tar.Z; 
   2. create a symbolic link to the resulting pdb_nat directory within the /tmp directory; 
   3. use the -pdb_paths=pdb_list option with hierview.

For example, run 'hierview natA_himsa 10 -pdb_paths=pdb_list' to generate output for the 10th subgroup.

For further information contact:
 Andrew F. Neuwald
 Institute for Genome Sciences and
 Department of Biochemistry & Molecular Biology
 University of Maryland School of Medicine
 801 West Baltimore St.
 BioPark II, Room 617
 Baltimore, MD 21201
 Tel: 410-706-6724; Fax: 410-706-1482; E-mail: aneuwald@som.umaryland.edu
 Home page: http://www.igs.umaryland.edu/~aneuwald