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134 lines
4.9 KiB
HTML
134 lines
4.9 KiB
HTML
<h1>NAME</h1>
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<p>mkdssp - Assign secondary structure to proteins</p>
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<h1>SYNOPSIS</h1>
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<p>mkdssp [OPTION] input [output]</p>
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<h1>DESCRIPTION</h1>
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<p>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 <strong>not</strong> predict
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secondary structure.</p>
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<p>The original DSSP program wrote output in a fixed format, this
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version by default writes annotated mmCIF files, storing the secondary
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structure information in the _struct_conf category.</p>
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<p>Since version 4.0 the mkdssp program also assigns PPII helices.</p>
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<h1>OPTIONS</h1>
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<p>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. E.g.
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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</p>
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<p>The output is optional, if omitted the output is written to
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<em>stdout</em>. If the name of the output file ends with either
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<em>.gz</em> or <em>.bz2</em> the output is compressed accordingly.</p>
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<dl>
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<dt><strong>--output-format</strong>=[dssp|mmcif]</dt>
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<dd>
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<p>If an output file is specified, the extension of the filename is used
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to choose to output format, but if it is unclear, mmcif is the default.
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Use this option to force output in either the old fixed column DSSP
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format or the new annotated mmCIF format.</p>
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</dd>
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<dt><strong>--no-dssp-categories</strong></dt>
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<dd>
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<p>When writing mmCIF files, suppress the output of all dssp_
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categories.</p>
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</dd>
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<dt><strong>--min-pp-stretch</strong></dt>
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<dd>
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<p>This option can be used to define the minimal number of residues with
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PHI/PSI angles within the range required to assing a PP helix.</p>
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</dd>
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<dt><strong>--write-other</strong></dt>
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<dd>
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<p>By default the new format does not write the structure information
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for OTHER. Use this flag to change that.</p>
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</dd>
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<dt><strong>--components</strong></dt>
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<dd>
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<p>The knowledge of compounds is loaded from the CCD file
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<em>components.cif</em> that should have been installed by
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<em>libcifpp</em>. You can override that file by using this option.</p>
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</dd>
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<dt><strong>--extra-compounds</strong></dt>
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<dd>
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<p>As an addition to the standard <em>components.cif</em> file, you can
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add more files using this option. Files should be either in CCD format
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or should be CCP4 restraints files.</p>
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</dd>
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<dt><strong>--mmcif-dictionary</strong></dt>
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<dd>
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<p>The default mmCIF dictionary file is installed by the
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<em>libcifpp</em> library but you can override it using this option.</p>
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</dd>
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</dl>
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<h1>DETAILS</h1>
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<p>The DSSP algorithm assings secondary structure based on the energy
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calculated for H-bonds.<br />
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<strong>Table 1. Secondary Structures recognized</strong></p>
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<table>
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<tbody>
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<tr class="odd">
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<td style="text-align: center;">DSSP Code</td>
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<td style="text-align: center;">mmCIF Code</td>
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<td style="text-align: center;">Description</td>
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</tr>
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<tr class="even">
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<td style="text-align: center;">H</td>
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<td style="text-align: center;">HELX_RH_AL_P</td>
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<td style="text-align: center;">Alphahelix</td>
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</tr>
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<tr class="odd">
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<td style="text-align: center;">B</td>
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<td style="text-align: center;">STRN</td>
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<td style="text-align: center;">Betabridge</td>
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</tr>
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<tr class="even">
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<td style="text-align: center;">E</td>
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<td style="text-align: center;">STRN</td>
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<td style="text-align: center;">Strand</td>
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</tr>
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<tr class="odd">
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<td style="text-align: center;">G</td>
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<td style="text-align: center;">HELX_RH_3T_P</td>
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<td style="text-align: center;">Helix_3</td>
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</tr>
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<tr class="even">
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<td style="text-align: center;">I</td>
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<td style="text-align: center;">HELX_RH_PI_P</td>
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<td style="text-align: center;">Helix_5</td>
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</tr>
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<tr class="odd">
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<td style="text-align: center;">P</td>
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<td style="text-align: center;">HELX_LH_PP_P</td>
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<td style="text-align: center;">Helix_PPII</td>
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</tr>
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<tr class="even">
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<td style="text-align: center;">T</td>
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<td style="text-align: center;">TURN_TY1_P</td>
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<td style="text-align: center;">Turn</td>
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</tr>
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<tr class="odd">
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<td style="text-align: center;">S</td>
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<td style="text-align: center;">BEND</td>
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<td style="text-align: center;">Bend</td>
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</tr>
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<tr class="even">
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<td style="text-align: center;">' ' (space)</td>
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<td style="text-align: center;">OTHER</td>
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<td style="text-align: center;">Loop</td>
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</tr>
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</tbody>
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</table>
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<h1>BUGS</h1>
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<p>The mmCIF format currently lacks a lot of information that was
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available in the old format like information about the bridge pairs or
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the span of the various helices recognized. Also the accessibility
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information is left out.</p>
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<p>If you think this information should be part of the output, please
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contact the author.</p>
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<h1>AUTHOR</h1>
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<p>Written by Maarten L. Hekkelman <maarten@hekkelman.com></p>
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<h1>REPORTING BUGS</h1>
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<p>Report bugs at https://github.com/PDB-REDO/dssp/issues</p>
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