weight/_dep/dssp/doc/mkdssp.1

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