From beroza ^%at%^ scripps.edu Wed May 21 13:01:01 1997 Received: from relay1.scripps.edu for beroza -8 at 8- scripps.edu by www.ccl.net (8.8.3/950822.1) id MAA06723; Wed, 21 May 1997 12:37:36 -0400 (EDT) Received: from euler.scripps.edu (euler.scripps.edu [137.131.252.34]) by relay1.scripps.edu (8.8.5/TSRI-1.5) with ESMTP id JAA08973 for ; Wed, 21 May 1997 09:37:35 -0700 (PDT) Received: (from beroza ^at^ localhost) by euler.scripps.edu (8.8.5/TSRI-1.4) id JAA28032 for chemistry %-% at %-% www.ccl.net; Wed, 21 May 1997 09:37:10 -0700 (PDT) Date: Wed, 21 May 1997 09:37:10 -0700 (PDT) From: Paul Beroza Message-Id: <199705211637.JAA28032#* at *#euler.scripps.edu> To: chemistry*- at -*www.ccl.net Subject: 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 --------------------------------------------------------------------- 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 ---------------------------------------------------------------------