3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>PDB Viewing</title>
27 <strong>Discovering and Viewing PDB and 3D-Beacons structures</strong>
29 Jalview can be used to explore the 3D structures of sequences in an
30 alignment by following the steps below:
32 <li>Select the <strong>"3D Structure Data..."</strong> option
33 from a sequence's <a href="../menus/popupMenu.html">pop-up
34 menu</a> to open the <a href="structurechooser.html">Structure
35 Chooser</a> dialog box.
37 <li>If one or more structures exist in the PDB for the given
38 sequence, the <a href="structurechooser.html">Structure
39 Chooser</a> dialog will open with them listed in the results
42 <li>However, if no structure was found, the <a
43 href="structurechooser.html">Structure Chooser</a> interface
44 will present options for manual association of PDB structures.
47 Since Jalview 2.11.2 you can also search the 3D-Beacons Network
48 for structures. The 3D-Beacons Network acts as a one-stop shop for protein
49 structures by combining and standardising data from several providers.
50 See <a href="structurechooser.html#3dbeaconssearch">3D-Beacons Search</a> for
55 <li><strong>Selecting PDB Structures</strong><br />
56 If one or more structures have been found from the PDB, you can select
57 the structures that you want to open and view by selecting them
58 with the mouse and keyboard.<br />By default, if structures were
59 discovered, then some will already be selected according to the
60 criteria shown in the drop-down menu. The default criteria is
61 'highest resolution', simply choose another to pick structures in
62 a different way.<br />
64 <li><strong>Viewing Cached Structures</strong><br />If
65 previously downloaded structures are available for your
66 sequences, the structure chooser will automatically offer them
67 via the <strong>Cached Structures</strong> view. If you wish
68 to download new structures, select one of the PDBe selection
69 criteria from the drop-down menu.</li>
71 <li><strong>To view selected structures, click the <strong>"View"</strong>
75 <li>Additional structure data will be downloaded with the
76 EMBL-EBI's dbfetch service</li>
77 <li><a href="siftsmapping.html">SIFTS</a> records will also
78 be downloaded for mapping UniProt protein sequence data to PDB
80 <li>A new structure viewer will open, or you will be
81 prompted to add structures to existing viewers (see <a
82 href="#afterviewbutton">below</a> for details).
87 <strong>Structure Viewers in the Jalview Desktop</strong><br /> The
88 <a href="jmol.html">Jmol viewer</a> has been included since Jalview
89 2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>,
90 provided it is installed and can be launched by Jalview. ChimeraX and <a href="pymol.html">PyMOL</a>
91 support is included from Jalview 2.11.2. The default
92 viewer can be configured in the <a href="preferences.html#structure">Structure
93 tab</a> in the <strong>Tools→Preferences</strong> dialog box.
96 Structure data imported into Jalview can also be processed to
97 display secondary structure and temperature factor annotation. See
98 the <a href="xsspannotation.html">Annotation from Structure</a> page
103 name="afterviewbutton">Controlling where the new structures
104 will be shown</a></strong>
106 <img src="schooser_viewbutton.png" />
107 <br />The Structure Chooser offers several options
108 for viewing a structure. <br/>
109 The <strong>Open new structure view</strong> button will open a new
110 structure viewer for the selected structures, but if there are views
111 already open, you can select which one to use, and press the <strong>Add</strong>
112 button. Jalview can automatically superimpose new structures based
113 on the linked alignments - but if this is not desirable, simple
114 un-tick the <strong>Superpose Structures</strong> checkbox.
118 <em>Superposing structures</em><br />Jalview superposes structures
119 using the currently selected columns (if more than 3 columns are
120 selected), or the visible portions of any associated sequence
121 alignments. Depending on the viewer, Root Mean Squared Deviation (RMS
122 or RMSD) for each pair of superpositions may be output in the
123 structure viewer's console.
125 <p>A message in the structure viewer's status bar will be shown if
126 not enough aligned columns were available to perform a superposition.
129 See the <a href="jmol.html">Jmol</a>, <a href="chimera.html">Chimera/X</a>
130 and <a href="pymol.html">Pymol</a> help pages for more information
131 about their individual capabilities.
134 <strong>Retrieving sequences from the PDB</strong><br>You can
135 retrieve sequences from the PDB using the <a
136 href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
137 retrieved with this service are derived directly from the PDB 3D
138 structure data, which can be viewed in the same way above. Secondary
139 structure and temperature factor annotation can also be added. <br />
141 <br>Jalview will also read PDB files directly - either in PDB
142 format, or <a href="mmcif.html">mmCIF</a>. Simply load in the file
143 as you would an alignment file. The sequences of any protein or
144 nucleotide chains will be extracted from the file and viewed in the
149 <strong>Associating a large number of PDB files to
150 sequences in an alignment</strong><br /> It is often the case when working
151 with structure alignments that you will have a directory of PDB
152 files, and an alignment involving one or more of the structures. If
153 you drag a number of PDB files onto an alignment in the Jalview
154 desktop, Jalview will give you the option of associating PDB files
155 with sequences that have the same filename. This means, for example,
156 you can automatically associate PDB files with names like '1gaq.pdb'
157 with sequences that have an ID like '1gaq'. <br /> <em>Note:
158 This feature was added in Jalview 2.7</em>
161 <em>Note for Jalview applet users:<br> Due to the applet
162 security constraints, PDB Files can currently only be imported by
163 cut and paste of the PDB file text into the text box opened by the
164 'From File' entry of the structure menu.
169 <strong>Viewing the PDB Residue Numbering</strong><br>
170 Sequences which have PDB entry or PDB file associations are
171 annotated with sequence features from a group named with the
172 associated PDB accession number or file name. Each feature gives the
173 corresponding PDB Residue Number for each mapped residue in the
174 sequence. The display of these features is controlled through the <strong>"View→Sequence
175 Features"</strong> menu item and the <a href="featuresettings.html">Feature
176 Settings dialog box</a>.
181 <strong>Switching between mmCIF and PDB format for
182 downloading files from the PDB</strong><br /> Jalview now employs the <a
183 href="mmcif.html">mmCIF format</a> for importing 3D structure data
184 from flat file and EMBL-PDBe web-service, as recommended by the
185 wwwPDB. If you prefer (for any reason) to download data as PDB files
186 instead, then first close Jalview, and add the following line to
187 your .jalview_properties file:<br />
188 <code> PDB_DOWNLOAD_FORMAT=PDB </code>
189 <br /> When this setting is configured, Jalview will only request
190 PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
191 file support was added in Jalview 2.10.</em>
195 <em><strong>Outstanding problem with cut'n'pasted
196 files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
197 via the cut'n'paste dialog box will not be correctly highlighted
198 or coloured when they are displayed in structure views, especially
199 if they contain more than one PDB structure. See the bug report at
200 http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>