Index of /~jba/CaPPS

      Name                    Last modified       Size  Description

[DIR] Parent Directory 30-Apr-2013 14:49 - [   ] Blas.tar.gz 01-Dec-2008 16:54 64k [DIR] Samples/ 06-Jan-1999 14:09 - [CMP] blasroutines.tar.Z 06-Jan-1999 14:10 119k [   ] copyright 06-Jan-1999 14:10 1k [   ] literature 16-Apr-1999 11:20 1k [CMP] main.tar.Z 01-Feb-2000 10:05 25k [CMP] subroutines.tar.Z 06-Jan-1999 14:10 103k


Calculated Peptide and Protein Spectra (CaPPS) Package Version 2.0

by Jon Applequist, Kimberly A. Bode, Mark L. Olson, and Kenneth
R. Sundberg, with contributions from James J. Coyle, Bernard
K.-K. Fung, Harsha Kudigram, Kathryn A. Thomasson, and Lucy C. Weiss.

------------------------------------------------------------------------

This set of programs enables one to calculate the ultraviolet
absorption and circular dichroic spectra of proteins based on PDB
coordinate files and other user-created peptides containing alpha
amino acid or beta amino acid residues. The theory is that of the
dipole interaction model developed in Dr. Applequist's group.  The
programs are designed to run on a Unix system with the f90 Fortran
compiler.

------------------------------------------------------------------------

The CaPPS directory contains the following .tar files, which will
download to your computer when you click on the directory item:

    main.tar.Z, subroutines.tar.Z, blasroutines.tar.Z

To decompress and undo the tar, type:

    uncompress <name.tar.Z>
    tar xvf <name.tar> 

The .tar file can be deleted once the individual files are successfully
unpacked.

------------------------------------------------------------------------

The file main.tar.Z contains a total of 11 files:

    capps.f: source code for CAlulated Peptide and Protein Spectra 
    scanpdb.f: code for program to define peptide fragments based on
               information in the pdb file
    wrtpdbscript.f: code for program to write user-defined peptide
               fragments
    readpdb.f: code to produce torsion angles and reference coordinates
               for the capps program
    splitfile.f: code to read molecule fragments and write out separate
               files for helix, sheet, and turn fragments
    wrtcappscript.f: code to write a scriptfile for capps
    checkformat.f: code for program to check input file format
    runn: executes the capps program
    jobnum: file used by runn to name the capps output, RENAME as .jobnum
    instructions: details on how to use each program
    copyright: copyright information

------------------------------------------------------------------------

The file subroutines.tar.Z contains 79 subroutine files.  Compile the
individual files with the command:

    f90 -c *.f

Create an archive file with:

    ar ru <archive.a>

Add the files to the archive with:

    ar -q <archive.a> *.o

Create the archive directory with:

    ar -t <archive.a>

Delete files from the archive with:

    ar -d <archive.a>

The .o files may be deleted once archived.

------------------------------------------------------------------------

The file blasroutines.tar.Z contains 61 blas and lapack subroutines
for those who do not have the blas/lapack library.  Compile the
individual files and archive them as above.  

Note: these routines are the public domain versions from
www.netlib.org. We find them to run more slowly on the Digital
platform than versions in the Digital Extended Math Library (DXML).

Update note (12/1/08): A user has reported that the Blas function
IDAMAX is missing from the file blasroutines.tar.Z, and that an error
message to this effect appears on running his f90 compiler on capps.f.
The new file Blas.tar.gz contains idamax.f as well as all the
subroutines in blasfiles.tar.Z.
------------------------------------------------------------------------
Questions? Email to jbaATiastate.edu (change AT to @)