README file for NasT

NAST (Nucleic Acid Simulation Tool) is a knowledge-based coarse-grained 
  tool for modeling RNA structures. It uses user-provided information about 
  primary sequence, secondary structure, and tertiary contacts (options) 
  of an RNA molecule to produce a diverse set of 3D structures that satisfy 
  these constraints. MAST currently only runs on LINUX.

INPUTS:

*Primary sequence file (required): One residues name per line. One 
  character per residue (A, U, C or G). Numer of lines in file is 
  same as number of residues in molecule. File name should be 
  *-primary.txt where * is the moelcule/project name. Example file: 
  6TNA-primary.txt. This file name must be correctly referenced in the *-params.py 
  file (for example 6TNA-params.py).

* Secondary structure file (required): First line is "#76" where the 
  number is the number of residues in the structure (76 is for tRNA). 
  Each next line defines a helix in the format "Name Start End Length". 
  For example "H1 1 76 4" is a helix where the first base pair is 
  between residues 1 and 76, and is 4 base pairs long. File name 
  should be *-SS.txt where * is the molecule/project name. 
  Example file: 6TNA-SS.txt. This file name must be correctly referenced 
  in the *-params.py file.

* Tertiary contacts file (options): Format "res1 res2 distance strength". 
  Where distance is in Angstroms. One pair per line. Example "1 48 13.7 50" 
  will put a spring between residues 1 and 48 with minimum engergy at
  distance 13.7 Angstroms with spring strength 50. File name should have 
  format *-PT.txt. Example file 6TNA-PT.txt. This file name must be 
  correctly referenced in the *-params.py file.

OUTPUT:

* A PDB (Protein Databank) file containing 3D structures that attempt to 
  satisfy the secondary and tertiary structure constraints applied (they
  still need to be filtered for tertiary contact satisfaction). You can
  visualize the structures using a program like VMD.
* A .psf file that connects the residues when loaded on top of the .pdb file
  in VMD.

Distribution Structure:
README       -- This file
LICENSE      -- Fancy talk for "BSD-like"
MANIFEST.in  -- Tells distutils what files to add to the distribution
setup.py     -- Installation file
nast/      -- The main code base
nast/md    -- The md code
examples/example1_trna   -- An example using the tRNA molecule

REQUIREMENTS FOR INSTALLATION:

NasT requires Python 2.3 or better (http://www.python.org), Numerical Python
  (http://numpy.sf.net), and NAST (http://simtk.org):

Please refer to the wiki at http://wiki.simtk.org/nast
  for complete instructions.

For a quick start:
Installing Python (http://python.org)
  Type 'python' from the unix/linux command line.  Look for Python 2.x[.x]
  We recommend that you install a version of python in your home directory
  instead of the default location.
  Install python in your home directory by using the following commands:
  './configure --prefix=$HOME'
  'make'
  'make install'

  You may need to add the your home directory to the beginning of your
  path, so that the locally installed python is used.
  For a bash shell, add the following line:
  'PATH=$HOME/bin:$PATH'

Also requires Numerical Python (http://numpy.sf.net):
  From the python prompt, type 'import Numeric'. No error means it's installed.

  To install Numeric correctly, download latest Numeric rpm or tar.gz file
  (do *not* use numarray or numpy) and follow directions.
  If you cannot find Numeric online, you can download it from 
  https://simtk.org/home/nast under the "Downloads" catagory.

  If you have installed python locally, use the following command:
  'python setup.py install'

  Otherwise, you can install Numeric in your home directory by using:
  'python setup.py install --prefix=$HOME'

  And finally, you *may* need to tell python where to find the files by
  setting the PYTHONPATH. This is not necessary is you originally installed
  python in your home directory.
   For csh-like shells and python2.3, might try adding
   the following to your .cshrc
      setenv PYTHONPATH "${HOME}/lib/python2.3/site-packages/Numeric"
   or, if PYTHONPATH exists:
      setenv PYTHONPATH "${PYTHONPATH}:${HOME}/lib/python2.3/site-packages/Numeric"

  Some Linux distributions hang while running some Numeric routines.
  A simple way to fix this is turn off all compiler optimizations by
  changing a line in "customize.py" from the following:
    extra_compile_args = ['']
    to
    extra_compile_args = ['-O0']   # Note that this is the letter 'o'
                                   # followed by the number zero


To install NasT, uncompress and untar NasT archive file:
    'gunzip -c nast.tar.gz | tar xvf -'

Then change to new directory and run the setup script to do install:
    'cd nast-x.x.x'

Then run the setup script to build and install NasT:
    'python setup.py build'
    'python setup.py install'

If this works, you are done!  Look around the examples directory and
try running one of them:
   'sh 1gidExample.sh' in the 1gidBuild folder
   'sh 6tnaExample.sh' in the 6tnaBuild folder

As with Numeric, you may be unable to the default location, 
  so try installing in your home directory:
If you do not have super-user privileges, 
  try installing in your home directory:
  'python setup.py install --prefix=$HOME'
And last, tell python where to find the files by setting the PYTHONPATH.
 For csh-like shells and python2.3, try adding the following to your .cshrc
    setenv PYTHONPATH "${HOME}/lib/python2.3/site-packages"
 or, if PYTHONPATH exists:
    setenv PYTHONPATH "${PYTHONPATH}:${HOME}/lib/python2.3/site-packages"

ADDITIONAL INFORMATION

Please see the Wiki at http://wiki.simtk.org/nast for instructions
  on installing and running NAST.

Addition help may be obtained via the discussion forum at
  http://simtk.org/nast (Click on Advanced -> Public Forums.