Other secondary structure tools

BMERC : needle tools : programs : Other SS programs

The following programs interpret and manipulate secondary structure information. At BMERC, for the most part, we use the DSSP program of Kabsch and Sander to define secondary structure.

Table of contents

  1. Other secondary structure tools
    1. Table of contents
    2. make-pdb-segs.pl
    3. compare-segs.pl
    4. make-ss-designations

make-pdb-segs.pl

make-pdb-segs.pl extracts the SHEET and HELIX records out of a PDB file on the standard input and generates a segment definition file on the standard output. The PDB file must also have the ATOM records present (in the usual order of HELIX, then SHEET, then ATOM) so it can use them to collate the secondary structure elements on output.

Usage: 

    make-pdb-segs.pl < pdb-file > seg-file

Known bugs:

  1. Certain pathologies of PDB file secondary structure definition (e.g. defining residues as part of two distinct strands in different sheets) are not detected, leading to overlapping strands in some cases. make-core.pl will detect such cases, but the error message will be something like "Can't find residue XYZ" when it really means it can't find the second occurrence of XYZ. -- rgr, 9-Sep-96.
  2. Barrels are identified via "Cn" (where n is generated sequentially for each barrel) rather than the "Cxxyyzz" style required by the official definition of segment designators.
  3. The PDB HELIX record specification defines nine different "helix types" in addition to the default (and standard) right-handed alpha helix (type 1). make-pdb-segs.pl designates this most popular type by "H", and all others by "Hn", where n is the numeric helix type. [It might save some trouble if we had an option to discard 3-10 helices (type 5) altogether. -- rgr, 9-Sep-96.]

compare-segs.pl

When given two segment definition files named on the command line, compare-segs.pl compares the two, producing a segment-by-segment report of alignments on the standard output. [Under development. -- rgr, 7-Sep-96.] [Still under development. -- rgr, 17-Sep-97.]

Usage: 

    compare-segs.pl locus pdb-file file1.seg file2.seg
The PDB file is needed in order to compute lengths and alignment errors in sequence space.

[need to define the output. probably something verbose and tab-delimited, from which other programs can generate readable reports. -- rgr, 7-Sep-96.]

make-ss-designations

Given "ss" format input on the standard input, make-ss-designations produces a segment definition format file on the standard output.

Usage: 

    make-ss-designations [ seg-file ] < ss-file

Arguments:

seg-file
name of the segment definition format file) on which to write output. If omitted, or given as "-", then the results are sent to the standard output.
ss-file
an "ss" format input file, as produced by the -ss option to the dssp4.pl program. This must be piped to make-ss-designations on the standard input; it cannot be named on the command line.
make-ss-designations converts the more-or-less raw per-residue secondary structure and strand residue adjacency information into a form that make-core.pl can use to produce core files. [The current, confusing convention for these files is to use the extension ".dssp" because that is usually the source of the SS data. -- rgr, 12-Aug-96.] Most of the hair is in deciding which sheet or barrel each strand belongs, based on the adjacency information. [should say much more here. -- rgr, 15-Jan-98.]

The undocumented make-ss-designations.lisp software is in charge of encoding strand adjacency information into segment designators. Most of the warning messages are generated by make-ss-designations.lisp, and concern such things as sheets or barrels that involve more than one chain, and degenerate sheets introduced by dssp4.pl when it eliminates short strands.

Warnings:

Known bugs:

  1. *** There are a number of parameters within the guess-ss-designations.lisp code, but make-ss-designations provides no way to change their defaults.
Bob Rogers <rogers@darwin.bu.edu>
Last modified: Thu Apr 6 16:13:21 EDT 2000