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2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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7 # Jalview is free software: you can redistribute it and/or
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20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
36 <head><title>PDB Viewing</title></head>
38 <p><strong>Viewing PDB Structures</strong></p>
39 <p>Jalview can view protein structures associated with a sequence via the <strong>"Structure→View
40 PDB entry:"</strong> entries from a sequence's <a
41 href="../menus/popupMenu.html">pop-up menu</a>. This will open an
42 interactive display of the structure in a new window, or prompt you
43 to associate the sequence with an existing view of the selected
44 structure. See the <a href="jmol.html">Jmol PDB viewer</a> help page
45 for more information about the display.
47 <p>To associate PDB files with a sequence, right click on a sequence ID and select
48 "Structure<strong>→</strong> Associate Structure with Sequence",
49 and one of the submenus:</p>
51 <li>From File - You can load a PDB file from the local machine or network and
52 associate it with the selected sequence. PDB files associated in this way
53 will also be saved in the <a href="jalarchive.html">Jalview Archive file</a>. <br>
55 <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch
56 the PDB file with the entered Id.<br>
58 <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover
59 PDB ids for all the sequences in the alignment which have valid Uniprot names
60 / accession ids. </li>
62 <p><strong>Importing PDB Entries or files in PDB format</strong><br>
63 You can retrieve sequences from the PDB using the <a
64 href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this
65 service are automatically associated with their source database entry. For PDB
66 sequences, simply select PDB as the database and enter your known PDB id (appended
67 with ':' and a chain code, if desired).
68 <br>Jalview will also read PDB files directly. Simply load in the file
69 as you would an alignment file. The sequences of any peptide chains
70 will be extracted from the file and viewed in the alignment window.
71 <br><em>Note for jalview applet users: due to the applet security
72 constraints, PDB Files can currently only be imported by cut and paste
73 of the PDB file text into the text box opened by the 'From File' entry
74 of the structure menu.</p>
75 <p><strong>Viewing the PDB Residue Numbering</strong><br>
76 Sequences which have PDB entry or PDB file associations are annotated
77 with sequence features from a group named with the associated PDB
78 accession number or file name. Each feature gives the corresponding
79 PDB Residue Number for each mapped residue in the seuqence. The
80 display of these features is controlled through the
81 <strong>"View→Sequence Features"</strong> menu item
82 and the <a href="featuresettings.html">Feature Settings dialog