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Commit dcd16754 by Maarten L. Hekkelman
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Merge branch 'trunk' of github.com:PDB-REDO/dssp into trunk

parents 3b0f2706 66cb9f0e
Showing with 79 additions and 171 deletions
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<!-- <article>
<h2>Downloading the PDB-REDO software</h2>
<article>
<h2>Using the DSSP software locally</h2>
<p>If you want to run large sets of DSSP calculations you can install DSSP locally by:
<ul>
<li>Downloading the current <a href="https://pdb-redo.eu/dssp/others/mkdssp.gz">Linux and WSL binary</a></li>
<li>Building DSSP from <a href="https://github.com/PDB-REDO/dssp">source</a></li>
<li>Installing the <a href="https://launchpad.net/ubuntu/+source/dssp">Debian/Ubuntu package</a> (note that this version is a bit older)</li>
<li>Installing the <a href="https://www.ccp4.ac.uk/">CCP4 suite</a> that comes with (an older version of) DSSP</li>
</ul>
<p>If you are working with sensistive data you can install PDB-REDO locally on <a
href="https://pdb-redo.eu/others/pdb-redo.tar.bz2">Linux and WSL</a>.
You can also use it to run large sets of custom PDB-REDO jobs. Alternatively, you can use the
<a z2:href="@{/api-doc}">PDB-REDO API</a> to commit batches of custom calculations.
Use <code>mkdssp -h</code> to get a short help message on how to run DSSP. Alternatively, you can use the
<a z2:href="@{/api-doc}">DSSP API</a> to commit batches of calculations.
</p>
</article>
<article>
<h2>Downloading PDB-REDO entries</h2>
<h2>Downloading ready-made DSSP annotations</h2>
<p>You can download PDB-REDO entries using you favorite molecular graphics program or manually. You can also
download the entire databank at once. Below are some basic examples, more data from the PDB-REDO
databank is described underneath.</p>
<h2>Molecular graphics:</h2>
<ul>
<li><a href="http://www.yasara.org" target="_blank">YASARA</a> has a native PDB-REDO <a
href="http://www.yasara.org/pdbredo.htm" target="_blank">interface to show models</a>.
</li>
<li><a href="http://www.ccp4.ac.uk/MG/" target="_blank">CCP4mg</a> can download PDB-REDO models and
maps.</li>
<li><a href="http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/" target="_blank">(Win)COOT</a> also
has a native
PDB-REDO interface that shows models, maps, and a guided tour through the model changes.
</li>
For your convenience we have already run DSSP on the entire Protein Data Bank. All entries are available in <a z2:href="|@{/about}#mmCIF|">mmCIF format</a>
and, if they fit, in the <a z2:href="|@{/about}#DSSP|">legacy DSSP format.</a>
</ul>
<h2>Manual download (single entries) via the website or using <code>wget</code>:</h2>
<ul>
<li><code>wget https://pdb-redo.eu/db/9xyz/9xyz_final.pdb</code> downloads the fully optimised
(re-refined and
rebuilt) PDB file.
</li>
<li><code>wget https://pdb-redo.eu/db/9xyz/9xyz_final.mtz</code> downloads the MTZ files to generate
electron
density maps.
</li>
<li><code>wget https://pdb-redo.eu/db/9xyz.zip</code> downloads all files of a PDB-REDO entry.</li>
<li><code>wget https://pdb-redo.eu/dssp/9xyz.cif.gz</code> downloads annotated mmCIF file</li>
<li><code>wget https://pdb-redo.eu/dssp/9xyz.dssp</code> downloads the legacy DSSP file (if available)</li>
</ul>
<h2>Download entire PDB-REDO databank using <code>rsync</code>:</h2>
<h2>Download entire DSSP databank using <code>rsync</code>:</h2>
<ul>
<li><code>rsync -av rsync://rsync.pdb-redo.eu/pdb-redo/ pdb-redo/</code> downloads the entire archive.
<li><code>rsync -av rsync://rsync.pdb-redo.eu/dssp/ dssp/</code> downloads the entire archive.
</li>
</ul>
<h2>License</h2>
<p><a href="license.txt" z2:href="@{/license}">Here</a> you can find the data usage license.</p>
<p><a z2:href="@{/license}">Here</a> you can find the data usage license.</p>
</article>
<article>
<h2>PDB-REDO entry description</h2>
<p>Each PDB-REDO entry consists of a set of files that describe the structure model in different states
(original,
re-refined, and re-refined &amp; rebuilt). Some of the data is provided for easy data mining. The table
below shows
the typical URLs of the files for the fictitious entry <code>9xyz</code>.</p>
<br />
<table>
<thead>
<tr>
<th>Description</th>
<th>Typical URL (for fictitious entry 9xyz)</th>
</tr>
</thead>
<tbody>
<tr>
<td colspan="2" class="group">Atomic coordinates</td>
</tr>
<tr>
<td>Initial model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_0cyc.pdb.gz</code></td>
</tr>
<tr>
<td>Re-refined (only) model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_besttls.pdb.gz</code></td>
</tr>
<tr>
<td>Re-refined &amp; rebuilt structure model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.pdb</code></td>
</tr>
<tr>
<td>Re-refined &amp; rebuilt structure model with total B-factors (PDB)</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final_tot.pdb</code></td>
</tr>
<tr>
<td>Re-refined &amp; rebuilt structure model with total B-factors (mmCIF)</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.cif</code></td>
</tr>
<tr>
<td colspan="2" class="group">Electron density</td>
</tr>
<tr>
<td>Map coefficients for the original model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_0cyc.mtz.gz</code></td>
</tr>
<tr>
<td>Map coefficients for re-refined (only) model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_besttls.mtz.gz</code></td>
</tr>
<tr>
<td>Map coefficients for re-refined &amp; rebuilt structure model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.mtz</code></td>
</tr>
<tr>
<td colspan="2" class="group">Validation data</td>
</tr>
<tr>
<td>WHAT_CHECK report for initial model</td>
<td><code>https://pdb-redo.eu/db/9xyz/wo/pdbout.txt</code></td>
</tr>
<tr>
<td>WHAT_CHECK report for re-refined (only) model</td>
<td><code>https://pdb-redo.eu/db/9xyz/wc/pdbout.txt</code></td>
</tr>
<tr>
<td>WHAT_CHECK report for re-refined &amp; rebuilt model</td>
<td><code>https://pdb-redo.eu/db/9xyz/wf/pdbout.txt</code></td>
</tr>
<tr>
<td>Ligand and ligand interaction data for the initial and re-refined &amp; rebuilt structure
model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_ligval.json</code> (only for entries with ligands; <a
href="id_ligval.json.schema" z2:href="@{/schema/id_ligval.json.schema}">JSON Schema</a>)
</td>
</tr>
<tr>
<td>Map fitting scores for the initial model <br />(RSCC, RSR, EDIAm, OPIA)</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_0cyc.json.gz</code> (<a href="id_0cyc.json.schema"
z2:href="@{/schema/id_0cyc.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>Map fitting scores for the re-refined &amp; rebuilt model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.json</code> (<a href="id_final.json.schema"
z2:href="@{/schema/id_final.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>Data for model improvement sliders</td>
<td><code>https://pdb-redo.eu/db/9xyz/pdbe.json</code> (<a href="pdbe.json.schema"
z2:href="@{/schema/pdbe.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td colspan="2" class="group">Visual tools</td>
</tr>
<tr>
<td>COOT script to show model changes</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.py</code> (Python) or
<code>https://pdb-redo.eu/db/9xyz/9xyz_final.scm</code>
(Scheme)
</td>
</tr>
<tr>
<td colspan="2" class="group">Descriptive data</td>
</tr>
<tr>
<td>PDB-REDO statistics for data mining (crystal parameters, R-factors, validation scores, etc.)
</td>
<td><code>https://pdb-redo.eu/db/9xyz/data.json</code> (<a href="data.json.schema"
z2:href="@{/schema/data.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>List of homologous entries in PDB-REDO databank</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_available_homologs.json</code> (<a
href="id_available_homologs.json.schema"
z2:href="@{/schema/id_available_homologs.json.schema}">JSON Schema</a>)</td>
</tr>
<tr>
<td>DSSP analysis of the re-refined &amp; rebuilt model</td>
<td><code>https://pdb-redo.eu/db/9xyz/9xyz_final.dssp</code></td>
</tr>
<tr>
<td>Software versions of all programs used</td>
<td><code>https://pdb-redo.eu/db/9xyz/versions.json</code> (<a href="versions.json.schema"
z2:href="@{/schema/versions.json.schema}">JSON Schema</a>)</td>
</tr>
</tbody>
</table>
</article> -->
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<meta charset="UTF-8" />
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<title>DSSP</title>
</head>
<body class="site">
<nav z2:replace="~{menu :: navbar('about')}" />
<div class="container site-content">
<article>
<h2>General</h2>
<!-- <p>This is the DSSP web server. Before using it, please read the <a z2:href="@{/privacy-policy}">privacy policy</a>.</p> -->
</article>
<article>
<h2>Usage Policy</h2>
<p>Data files contained in the DSSP databank (rsync://rsync.pdb-redo.eu/dssp; <a
z2:href="@{/db}">https://pdb-redo.eu/dssp</a>) are free of all copyright restrictions and made fully
and freely available for both non-commercial and commercial use. Users of the data should attribute
DSSP, the Protein Data Bank and the original authors of that structural data. By using the materials available in the
DSSP databank, the user agrees to abide by the conditions described below:</p>
<ul>
<li>The archival data files in the DSSP databank are made freely available to all users. Data files
within the archive may be redistributed in original form without restriction. Redistribution of
modified data files is allowed only if the parent data file is attributed.</li>
<li>Where applicable, the usage policy of the parent PDB archive entries applies.</li>
<li>The data in the DSSP databank are provided on an "as is" basis. Neither DSSP nor its parent
or comprising institutions can be held liable to any party for direct, indirect, special,
incidental, or consequential damages, including lost profits, arising from the use of DSSP
materials.</li>
<li>Resources on pdb-redo.eu/dssp are provided without warranty of any kind, either expressed or implied.
This includes but is not limited to merchantability or fitness for a particular purpose. The
institutions managing this site make no representation that these resources will not infringe any
patent or other proprietary right.</li>
</ul>
</article>
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