Protein Structure: Internal coords --> PDB

Wayne Rindone rindone at ribo.harvard.edu
Mon Nov 2 15:51:08 EST 1992


>     I would be most grateful if you could help me locate a program that
>converts protein internal (dihedral angles: phi, psi, omega, chi's...)
>coordinate files into cartesian - PDB (Protein Data Bank) type files !
>     The program that does the reverse transformation is available from
>The Protein Data Bank...  

>Thank you,

>     Emil Marcus  V071RW4P at ubvms.cc.buffalo.edu    MARCUS at acsu.buffalo.edu

     One software package that might be useful in this regard is the
NIH-sponsored Prophet system for a variety of Unix workstations.

     Prophet includes an interactive procedure called makepolypeptide
that constructs a three dimensional structure from a series of amino
acid names, phi angles, and psi angles. It does not explicitly offer
prepackaged control over the omega and chi angles (all the omegas are
set to 180 degrees, chi angles are whatever was found in the template
residues). However, what is created is a Prophet molecule, for which
there are a variety of techniques, including interactive pointing as
well as procedure calls, for modifying torsion angles and other
geometric parameters. Prophet does know how to create a PDB-formatted
file for any Prophet molecule. 

     More information about Prophet can be obtained by sending email
to prophet-info at bbn.com

Wayne Rindone
Department of Cellular and Developmental Biology
Harvard University
rindone at nucleus.harvard.edu

Wayne Rindone
Department of Cellular and Developmental Biology

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