mapping sequence data onto know 2ndary structures

 A couple of weeks ago Dan Severance wrote:
 >   I want to be able to quickly generate a given secondary structure
 > from a sequence, and I'd like to do it nongraphically so I can generate
 > a large number with little or no "human" intervention :-)
 >    I'm not talking reality, per se, just a sequence and an identifier
 > of some sort specifying that I want a generic beta sheet, gamma turn,
 > etc.
 >    I know how to do it graphically in various software packages, but
 > I want to be able to generate these from an automated script.
 I wrote a program, "peptide",  to do this.  It is in the NAB language
 (which was designed for nucleic acids, but can also be used for proteins)
 The command line syntax is:
 % peptide  structure sequence < -lib libfile>
 where "structure" defines the type of structure to be created and
 "sequence" is a string o of 1 letter amino acid codes.  For example:
 % peptide ALPHA  AAAAA -lib conf.lib
 will write out (in pdb format) the coordinates of an alanine pentapeptide
 in an alpha helical structure.
 You must have the "nab" compiler:
   info on nab = http://www.scripps.edu/case.
   nab source  = ftp://ftp.scripps.edu/pub/macke/nab-2.1.tar.Z
 Once you have the nab compiler installed, get the peptide package from
 	ftp://ftp.scripps.edu/pub/beroza/peptide
 I hope this is useful, and any comments and suggestions about the
 program are welcome.
 Paul
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  Paul Beroza
  The Scripps Research Institute        email: beroza "-at-" scripps.edu
  Department of Molecular Biology       phone: 619-784-9957
  10550 N. Torrey Pines Rd. - TPC15     fax: 619-784-8896
  La Jolla, CA 92037                    URL: www.scripps.edu/~beroza
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