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95 lines
3.3 KiB
Groff
95 lines
3.3 KiB
Groff
.TH mkdssp 1 "2023-06-13" "version 4.3.2" "User Commands"
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.if n .ad l
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.nh
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.SH NAME
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mkdssp \- Assign secondary structure to proteins
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.SH SYNOPSIS
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mkdssp [OPTION] input [output]
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.SH DESCRIPTION
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The DSSP program was designed by Wolfgang Kabsch and Chris Sander to
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standardize secondary structure assignment. DSSP is a database of
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secondary structure assignments (and much more) for all protein entries
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in the Protein Data Bank (PDB). mkdssp is the program that calculates
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DSSP entries from PDB entries. mkdssp does \fBnot\fR predict secondary structure.
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.sp
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The original DSSP program wrote output in a fixed format, this version
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by default writes annotated mmCIF files, storing the secondary structure
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information in the _struct_conf category.
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.sp
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Since version 4.0 the mkdssp program also assigns PPII helices.
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.SH OPTIONS
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The input file can be either mmCIF or PDB format and the file may be
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gzip compressed. Note that input files must be formatted correctly.
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E.g. PDB files must have a CRYST1 record. More info:
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https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html#CRYST1
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.sp
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The output is optional, if omitted the output is written to \fIstdout\fR. If
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the name of the output file ends with either \fI.gz\fR or \fI.bz2\fR the
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output is compressed accordingly.
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.TP
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\fB--output-format\fR=[dssp|mmcif]
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If an output file is specified, the extension of the filename is used to
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choose to output format, but if it is unclear, mmcif is the default. Use
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this option to force output in either the old fixed column DSSP format or
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the new annotated mmCIF format.
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.TP
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\fB--no-dssp-categories\fR
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When writing mmCIF files, suppress the output of all dssp_ categories.
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.TP
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\fB--min-pp-stretch\fR
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This option can be used to define the minimal number of residues with PHI/PSI
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angles within the range required to assing a PP helix.
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.TP
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\fB--write-other\fR
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By default the new format does not write the structure information for OTHER.
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Use this flag to change that.
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.TP
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\fB--components\fR
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The knowledge of compounds is loaded from the CCD file \fIcomponents.cif\fR
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that should have been installed by \fIlibcifpp\fR. You can override that file
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by using this option.
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.TP
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\fB--extra-compounds\fR
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As an addition to the standard \fIcomponents.cif\fR file, you can add more
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files using this option. Files should be either in CCD format or should be
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CCP4 restraints files.
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.TP
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\fB--mmcif-dictionary\fR
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The default mmCIF dictionary file is installed by the \fIlibcifpp\fR library
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but you can override it using this option.
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.SH DETAILS
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The DSSP algorithm assings secondary structure based on the energy calculated
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for H-bonds.
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.br
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.B Table\ \&1.\ \&Secondary\ Structures\ recognized
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.TS
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allbox;
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cb cb cb .
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DSSP Code mmCIF Code Description
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.T&
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l l l.
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H HELX_RH_AL_P Alphahelix
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B STRN Betabridge
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E STRN Strand
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G HELX_RH_3T_P Helix_3
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I HELX_RH_PI_P Helix_5
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P HELX_LH_PP_P Helix_PPII
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T TURN_TY1_P Turn
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S BEND Bend
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T{
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\(aq \(aq (space)
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T} OTHER Loop
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.TE
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.SH BUGS
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The mmCIF format currently lacks a lot of information that was available
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in the old format like information about the bridge pairs or the span
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of the various helices recognized. Also the accessibility information
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is left out.
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.sp
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If you think this information should be part of the output, please contact
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the author.
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.SH AUTHOR
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Written by Maarten L. Hekkelman <maarten@hekkelman.com>
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.SH "REPORTING BUGS"
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Report bugs at https://github.com/PDB-REDO/dssp/issues
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