<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
<tocitem text="PDB Structure Chooser" target="pdbchooser" />
<tocitem text="Jmol Viewer" target="pdbjmol" />
- <tocitem text="Chimera Viewer" target="chimera" />
- <tocitem text="Simple PDB Viewer" target="pdbmcviewer" />
+ <tocitem text="Chimera Viewer" target="chimera" />
</tocitem>
<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
<tocitem text="VAMSAS Data Exchange" target="vamsas">
</strong><em> Colours each residue in the structure with the colour
of its corresponding residue in the associated sequence as
rendered in the associated alignment views, including any
- Uniprot sequence features or region colourings.<br />Pick
+ UniProt sequence features or region colourings.<br />Pick
which of the associated alignment views are used to colour
the structures using the <strong>View→Colour
by ..</strong> sub menu.
</li>
</ol>
<p>
- If your DAS source selection contains sources which use Uniprot
- accession ids, you will be asked whether Jalview should find Uniprot
+ If your DAS source selection contains sources which use UniProt
+ accession ids, you will be asked whether Jalview should find UniProt
Accession ids for the given sequence names. It is important to
- realise that many DAS sources only use Uniprot accession ids, rather
- than Swissprot/Uniprot sequence names.<br> The <a
+ realise that many DAS sources only use UniProt accession ids, rather
+ than Swissprot/UniProt sequence names.<br> The <a
href="../webServices/dbreffetcher.html"
>database reference fetcher</a> documentation describes how Jalview
discovers what database references are appropriate for the sequences
</strong><em> Colours each residue in the structure with the colour
of its corresponding residue in the associated sequence as
rendered in the associated alignment views, including any
- Uniprot sequence features or region colourings.<br />Pick
+ UniProt sequence features or region colourings.<br />Pick
which of the associated alignment views are used to colour
the structures using the <strong>View→Colour
by ..</strong> sub menu.
<title>mmCIF File Format</title>
</head>
<body>
- <strong>mmCIF File Format</strong>
- <p>The mmCIF file format (macromolecular Crystallographic
- Information) was developed under the auspices of the International Union of Crystallography (IUCr) to extend the Crystallographic Information
- File (CIF) data representation used for describing small molecule
- structures and associated diffraction experiments.</p>
- <strong>Merits of mmCIF file format</strong>
- <ul>
- <li>Large structures (containing >62 chains and/or 99999 ATOM
- records) that cannot be fully represented in the PDB file format are
- available in the PDB archive as single PDBx/mmCIF files.</li>
- <li>PDBx/mmCIF file format provides richer data annotation</li>
- <li>PDBx/mmCIF became the standard PDB archive format in 2014.
- Since 2016 the PDB File Format is no longer being modified or
- extended to support new content.
- </li>
- </ul>
+ <strong>What is mmCIF ?</strong>
+ <br />mmCIF stands for 'macro-molecular Crystallographic Information
+ File'. This format was developed by the PDB consortium and the
+ International Union of Crystallography (IUCr), based on
+ Crystallographic Information File (CIF), a format used for describing
+ the structures of small molecules.<br/>mmCIF became the recommended format
+ for the exchange of biomacromolecular structures in 2014.
+ <p>
+ <strong>mmCIF and Jalview</strong> <br />Since Jalview 2.10, mmCIF
+ is used for structures downloaded from the PDB. This means:
+ </p>
+ <ol>
+ <li>Jalview can use the mmCIF to read structures that are too
+ large to be represented by a single PDB file. (ie, with more than
+ >62 chains and/or 99999 ATOM records).</li>
+ <li>Jalview users will have access to the richer annotation
+ provided by PDBx/mmCIF files.</li>
+ <li>There may be slight differences between sequences
+ containing modified residues for structures downloaded in mmCIF
+ format. This is because mmCIF differs from the PDB format in the
+ way it describes non-standard sequence data.</li>
+ </ol>
- <em>mmCIF file format support for importing 3D structure data from
- flat file and EMBL-PDBe via mmCIF was added in Jalview 2.9.1</em>
+ <em>Support for importing 3D structure data from flat file and
+ EMBL-PDBe as mmCIF was added in Jalview 2.10</em>
</body>
</html>
\ No newline at end of file
</strong><em> Colours each residue in the structure with the colour
of its corresponding residue in the associated sequence as
rendered in the associated alignment view, including any
- Uniprot sequence features or region colourings.<br>
+ UniProt sequence features or region colourings.<br>
Residues which only exist in the PDB structure are coloured
white if they are insertions (relative to the associated
sequence in the alignment) and grey if they are N or C
<p>
Jalview can colour parts of a sequence based on the presence of
sequence features - which may be retrieved from database records
- (such as Uniprot), the result of <a href="search.html">sequence
+ (such as UniProt), the result of <a href="search.html">sequence
motif searches</a> or simply read from a <a href="featuresFormat.html">sequence
features file</a>. You can also <a href="creatinFeatures.html">create
features</a> from the results of searches or the current selection,
<p>
Since Jalview 2.08, sequence features assigned to a sequence can be
organised into groups, which may indicate that the features were all
- retrieved from the same database (such as Uniprot features), or
+ retrieved from the same database (such as UniProt features), or
generated by the same analysis process (as might be specified in a <a
href="featuresFormat.html"
>sequence features file</a>).
</p>
<p>If you use the WSDBFetch sequence fetcher services (EMBL,
- Uniprot, PFAM, and RFAM) in work for publication, please cite:</p>
+ UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
<p>
Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
<body>
<p>
<strong>Mapping Between Different Sequences</strong>
- </p>
+ </p><!-- TODO: review and check if this page is really needed -->
<p>A new feature in Jalview 2.3 is the ability to map between
sequences in different domains, based on alignment, or by the use of
explicit mappings provided by databases.</p>
correspondence between DNA and protein sequences. This mapping can
be imported directly from EMBL and EMBLCDS database records
retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>, and
- allows sequence features to be mapped directly from Uniprot das
+ allows sequence features to be mapped directly from UniProt das
sources to their coding region on EMBL sequence records.
</p>
- <p>In Jalview 2.9.1 <a href="siftsmapping.html">SIFTS Mapping</a> was added as a better means for explicitly identifying the coordinates corresponding to a displayed sequence when viewing a PDB structure associated with a sequence </p>
+ <em><a href="siftsmapping.html">SIFTS Mapping</a> between PDB and
+ UniProt data was introduced in Jalview 2.10</em>
</body>
</html>
<html>
<head>
<meta charset="UTF-8">
-<title>SIFTS Mapping</title>
+<title>SIFTS Mapping from UniProt for PDB Structures</title>
</head>
<body>
-
- <p><strong>SIFTS Mapping</strong></p>
-
+
<p>
- SIFTS (Structure Integration with Function, Taxonomy
- and Sequences) provides an up-to-date resource for residue-level
- mapping between Uniprot and PDB entries. The information is updated and
- released weekly simultaneously with the release of new PDB entries.
- SIFTS Entries are published as XML files and made publicly available via an FTP
- site hosted at the European Bioinformatics Institute.
+ <strong>SIFTS Mapping for UniProt sequences and PDB
+ Structures</strong><br /> SIFTS (Structure Integration with Function,
+ Taxonomy and Sequences) is a database of residue-level mappings
+ between UniProt protein sequences, and protein structures found in
+ the PDB. The database is updated for each PDB release, and is
+ provided by the <a href="https://www.ebi.ac.uk/pdbe/docs/sifts/">PDBe
+ at EMBL-EBI</a>.
</p>
-
+ <p>When Jalview imports PDB data for a protein sequence found in
+ UniProt, either via the 'View 3D Structure...' option, or the 'Fetch
+ DB Refs' web services menu, Jalview will also download its SIFTS
+ record and use that information to construct a mapping between the
+ sequence and downloaded structure.</p>
+ <p>If, for some reason, no SIFTS mapping data exists, then Jalview
+ will generate a mapping using its built-in Needleman and Wunsch
+ global alignment algorithm. This method of mapping was used for all
+ structures prior to version 2.10.
<p>
- At the point of viewing a PDB structure, if the default mapping method is set as 'SIFTS',
- Jalview will download a SIFTS file
- for the target entry and uses it to accurately map the sequence residues with the
- structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch
- Alignment algorithm to map sequence residues to structure residues, and that may not
- always result to a correct mapping since it is computational determined.
+ <strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
+ Configuration options controlling whether SIFTS mappings are used
+ can be found in the <strong>Tools → Preferences →
+ Structure tab</strong>, under 'Sequence ↔ Structure method'.<br /> <em>Note:</em>
+ Changing the configuration will only affect how new mappings are
+ created. In order to recompute mappings for structures already
+ loaded, please reload the sequence & structural data.
</p>
-
+
<p>
- <strong>Configuration</strong><br/>
- The default mapping method can be configured via <strong>Tools → Preferences →
- Structure tab</strong> Then scroll to the 'Sequence ↔ Structure method' section of
- the dialog box and change the default method. When 'SIFTS' is enabled as the default, all
- mappings between 'Sequence ↔ Structure' is performed via SIFTS provided that there
- is a valid SIFTS resource for the PDB entry. If no valid SIFTS resource is available, then
- the 'Sequence ↔ Structure' mapping falls back to Needleman and Wunsch Alignment algorithm.
- </p>
-
- <p><strong>Multi-Chain Mappings</strong>
- <br/>One of the main merits of SIFTS is the ability to accurately achieve multi-chain mapping
- (one-to-many) between a single Uniprot sequence and its corresponding multiple chains in
- PDB. Consequently, mousing over the uniprot sequence in the alignment window results
- to highlighting multiple corresponding positions in the structure viewer for the mapped chains.
+ <strong>Multi-Chain Mappings</strong> <br />SIFTS gives Jalview the
+ ability to display multi-chain mappings between UniProt sequences
+ and PDB structure data. This is important when working with
+ multimeric proteins, since the biological unit will contain several
+ structures for the same protein sequence. Multi-chain mapping allows
+ all residues in a structure to be located in the alignment, and
+ also, when shading the structure by sequence colours, enables
+ conservation patterns between oligomer interfaces to be explored.
</p>
+ <p>To see this in action, load uniprot sequence for FER1_MAIZE
+ then veiw PDB structure for 3B2F, you will notice that mousing over
+ the sequence results to two positions being highlighted in the
+ structure, also colouring the sequence transfers the color to all
+ the mapped chains in the structure.</p>
+
<p>
- To see this in action, load uniprot sequence for FER1_MAIZE then veiw PDB structure for 3B2F, you
- will notice that mousing over the sequence results to two positions being highlighted in the
- structure, also colouring the sequence transfers the color to all the mapped chains in the structure.
- </p>
-
+ <Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
+ by the SIFTS record is accessible via <strong>File →
+ View mapping</strong> menu of the structure viewers. The screenshot below
+ is the mapping output for the <Strong>{FER1_MAIZE ↔
+ 3B2F}</Strong> example described above, and confirms that all two chains
+ were mapped. The mapping method used can be seen within the area
+ highlighted with red boarder.
<p>
- <Strong>Viewing Mapping Output</Strong> <br/>
- The mapping output is accessible via <strong>File → View mapping</strong> menu of the structure
- viewers. The screenshot below is the mapping output for the <Strong>{FER1_MAIZE ↔ 3B2F}</Strong>
- example described above. Observe that all the two chains were mapped. The mapping method used can be
- seen within the area highlighted with red boarder. This is useful for visually ascertaining the
- mapping method when in doubt.
+
+  <img src="sifts_mapping_output.png" align="left"
+ alt="SIFTS mapping output" />
<p>
-
-  <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
-
-
- <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>
-
+ <em>SIFTS Mapping integration was added in Jalview 2.10</em>
+ </p>
+
</body>
</html>
\ No newline at end of file
structures using various metric categories avaialble from the
meta-data of the structures. To perform this simply select any of the
following options from the drop-down menu in the Structure Chooser
- interface: Best Uniprot coverage, Higest Resolution, Best Quality,
+ interface: Best UniProt coverage, Higest Resolution, Best Quality,
Highest Protein Chain etc. When the 'Invert' option is selected,
Jalview returns an inverse result for the current selected option in
the drop-down menu.
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
-<title>The Uniprot Free Text Search Interface</title>
+<title>The UniProt Free Text Search Interface</title>
</head>
<body>
- <strong>The Uniprot Free Text Search Interface</strong>
+ <strong>The UniProt Free Text Search Interface</strong>
+ <br /> Since version 2.10 (September 2016), the Jalview Desktop
+ provides a search interface for interactive discovery and retrieval of
+ sequence data from UniProt. This dialog enables UniProt sequence
+ metadata to be searched with free text and structured queries, which
+ allows sequences to be located via gene name, keywords, or even
+ <em>via</em> manual cross-referencing from UniProt or other
+ bioinformatics websites.
<p>
- Jalview provides a specialised interface that allows fast and
- efficient discovery and retrieval of data from the Uniprot database.
- It allows
- interactive querying of Uniprot metadata with free text and structured
- queries, so sequences can be located without prior knowledge of
- their database accessions, or <em>via</em> manual cross-referencing
- from Uniprot or other bioinformatics websites.
+ To open the UniProt Sequence Fetcher, select UniProt as the database
+ from any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened
+ <em>via</em> <strong>"File →Fetch
+ Sequences"</strong>).
</p>
<p>
- To open the UniProt Sequence Fetcher, select UniProt as the database from
- any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
- <strong>"File →Fetch Sequences"</strong>).
- </p>
- <p>
- <img src="uniprotseqfetcher.png" align="left"
- alt="Uniprot sequence fetcher (introduced in Jalview 2.9.1)"
- />
+ <img src="uniprotseqfetcher.png" align="left"
+ alt="UniProt sequence fetcher (introduced in Jalview 2.10)" />
</p>
<p>
- <strong>Searching the Uniprot Database</strong>
+ <strong>Searching the UniProt Database</strong>
</p>
<p>
- To search the Uniprot, begin typing in the text box. The results of your
- query are shown in the search results tab, which queries Uniprot after 1.5secs every time
- you type in the search text box. You can sort results according to
- the displayed columns, and select entries with the mouse or
- keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
- button to retrieve and visualise the sequences in Jalview Alignment interface.
+ To search UniProt, simply begin typing in the text box. After a
+ short delay (uabout 1.5 seconds), results will be shown in the table
+ below. You can sort results by clicking on the displayed columns,
+ and select entries with the mouse or keyboard. Once you have
+ selected one or more entries, hit the <strong>OK</strong> button to
+ retrieve the sequences.
</p>
<ul>
- <li><strong>Searching a specific Uniprot field </strong> If you
- want to find sequences based on a specific Uniprot metadata field,
- you can select it from the drop-down menu.</li>
-
+ <li><strong>Searching a specific UniProt field </strong> To
+ find sequences with particular UniProt metadata, you can select a
+ field to search from the drop-down menu.</li>
+
+
+ <li><strong>Bulk UniProt record retrieval</strong><br> To
+ retrieve several uniprot accessions at once, first select <strong>UniProt
+ ID</strong> from the dropdown menu, then paste in the accession IDs as a
+ semi-colon separated list. (e.g. fila_human; mnt_human;
+ mnt_mouse).<br />Hitting Return or OK will automatically fetch
+ those IDs, like the default Sequence Fetcher interface.</li>
- <li><strong>Bulk Uniprot retrieval</strong><br>
- Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon.
- e.g. fila_human; mnt_human; mnt_mouse.<br />Hitting Return or OK will automatically
- fetch those IDs, like the default Sequence Fetcher interface.</li>
-
- <li><strong>Advanced / Custom querying</strong>
- The table below provides a brief overview of the supported Uniprot query syntax (see <a href="uniprotqueryfields.html">query fields for UniProtKB</a>):
- <table border="1" width="95%">
- <tr>
- <td><code>human antigen</code></td>
- <td rowspan="3">All entries containing both terms.</td>
- </tr>
- <tr>
- <td><code>human AND antigen</code></td>
- </tr>
- <tr>
- <td><code>human && antigen</code></td>
- </tr>
- <tr>
- <td><code>"human antigen"</code></td>
- <td>All entries containing both terms in the exact order.</td>
- </tr>
- <tr>
- <td><code>human -antigen</code></td>
- <td rowspan="3">All entries containing the term <code>human</code>
- but not <code>antigen</code>.
- </td>
- </tr>
- <tr>
- <td><code>human NOT antigen</code></td>
- </tr>
- <tr>
- <td><code>human ! antigen</code></td>
- </tr>
- <tr>
- <td><code>human OR mouse</code></td>
- <td rowspan="2">All entries containing either term.</td>
- </tr>
- <tr>
- <td><code>human || mouse</code></td>
- </tr>
- <tr>
- <td><code>antigen AND (human OR mouse)</code></td>
- <td>Using parentheses to override boolean precedence rules.</td>
- </tr>
- <tr>
- <td><code>anti*</code></td>
- <td>All entries containing terms starting with <code>anti</code>.
- Asterisks can also be used at the beginning and within terms. <strong>Note:</strong>
- Terms starting with an asterisk or a single letter followed by an
- asterisk can slow down queries considerably.
- </td>
- </tr>
- <tr>
- <td><code> author:Tiger*</code></td>
- <td>Citations that have an author whose name starts with <code>Tiger</code>.
- To search in a specific field of a dataset, you must prefix your
- search term with the field name and a colon. To discover what
- fields can be queried explicitly, observe the query hints that are
- shown after submitting a query or use the query builder (see
- below).
- </td>
- </tr>
- <tr>
- <td><code>length:[100 TO *]</code></td>
- <td>All entries with a sequence of at least 100 amino acids.</td>
- </tr>
- <tr>
- <td><code>citation:(author:Arai author:Chung)</code></td>
- <td>All entries with a publication that was coauthored by two
- specific authors.</td>
- </tr>
- </table>
- </li>
-</ul>
+ <li><strong>Complex queries with the UniProt query
+ Syntax</strong> The text box also allows complex queries to be entered.
+ The table below provides a brief overview of the supported syntax
+ (see <a href="uniprotqueryfields.html">query fields for
+ UniProtKB</a>):
+ <table border="1" width="95%">
+ <tr>
+ <td><code>human antigen</code></td>
+ <td rowspan="3">All entries containing both terms.</td>
+ </tr>
+ <tr>
+ <td><code>human AND antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>human && antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>"human antigen"</code></td>
+ <td>All entries containing both terms in the exact order.</td>
+ </tr>
+ <tr>
+ <td><code>human -antigen</code></td>
+ <td rowspan="3">All entries containing the term <code>human</code>
+ but not <code>antigen</code>.
+ </td>
+ </tr>
+ <tr>
+ <td><code>human NOT antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>human ! antigen</code></td>
+ </tr>
+ <tr>
+ <td><code>human OR mouse</code></td>
+ <td rowspan="2">All entries containing either term.</td>
+ </tr>
+ <tr>
+ <td><code>human || mouse</code></td>
+ </tr>
+ <tr>
+ <td><code>antigen AND (human OR mouse)</code></td>
+ <td>Using parentheses to override boolean precedence
+ rules.</td>
+ </tr>
+ <tr>
+ <td><code>anti*</code></td>
+ <td>All entries containing terms starting with <code>anti</code>.
+ Asterisks can also be used at the beginning and within
+ terms. <strong>Note:</strong> Terms starting with an
+ asterisk or a single letter followed by an asterisk can slow
+ down queries considerably.
+ </td>
+ </tr>
+ <tr>
+ <td><code> author:Tiger*</code></td>
+ <td>Citations that have an author whose name starts with
+ <code>Tiger</code>. To search in a specific field of a
+ dataset, you must prefix your search term with the field
+ name and a colon. To discover what fields can be queried
+ explicitly, observe the query hints that are shown after
+ submitting a query or use the query builder (see below).
+ </td>
+ </tr>
+ <tr>
+ <td><code>length:[100 TO *]</code></td>
+ <td>All entries with a sequence of at least 100 amino
+ acids.</td>
+ </tr>
+ <tr>
+ <td><code>citation:(author:Arai author:Chung)</code></td>
+ <td>All entries with a publication that was coauthored by
+ two specific authors.</td>
+ </tr>
+ </table></li>
+ </ul>
<p>
<strong>Result pagination</strong>
</p>
- The query results returned from the Uniprot server are paginated for performance optimisation.
- The button labelled <strong>' << '</strong> and <strong>' >> '</strong> can be used to navigate to the next or previous result page respectively.
- The page range is shown on the title bar of the Free Text Search interface. Jalview's pagination implementation supports multiple selection of entries across multiple pages.
-
-
- <p>
- <strong>Customising The Uniprot Sequence Fetcher</strong>
- </p>
+ The query results returned from the UniProt server are paginated for
+ performance optimisation. The button labelled
+ <strong>' << '</strong> and
+ <strong>' >> '</strong> can be used to navigate to the
+ next or previous result page respectively. The page range is shown on
+ the title bar of the Free Text Search interface. Jalview's pagination
+ implementation supports multiple selection of entries across multiple
+ pages.
+
+
<p>
- To change the displayed meta-data in the search result, click the
- 'Customise Displayed Options' tab, and select the fields you'd like
- to displayed or remove.
+ <strong>Customising The UniProt Sequence Fetcher</strong>
</p>
+ <p>To change the displayed meta-data in the search result, click
+ the 'Customise Displayed Options' tab, and select the fields you'd
+ like to displayed or remove.</p>
<p>
- <em>The Uniprot Free Test Search Interface was introduced in
- Jalview 2.9.1</em>
+ <em>The UniProt Free Test Search Interface was introduced in
+ Jalview 2.10.0</em>
</p>
</body>
</html>
\ No newline at end of file
</head>
<body>
<p>
- <strong>Viewing PDB Structures</strong>
+ <strong>Discovering and Viewing PDB Structures</strong>
</p>
- Jalview can be used to view protein structures by following the steps
- below:
+ Jalview can be used to explore the 3D structures of sequences in an
+ alignment by following the steps below:
<ol>
<li>Select the <strong>"3D Structure Data..."</strong> option
from a sequence's <a href="../menus/popupMenu.html">pop-up
pane.
</li>
<li>However, if no structure was found, the <a
- href="structurechooser.html"
- >Structure Chooser</a> interface will present options for manual
- association of PDB structures.
+ href="structurechooser.html">Structure Chooser</a> interface
+ will present options for manual association of PDB structures.
</li>
</ul>
</li>
- <li><strong>Selecting Structures</strong><br /> If structures
- have been discovered, then some will already be selected according
- to predefined selection criteria, such as structures with the
- highest resolution. Use the drop down menu to select structures
- according to different criteria, or, alternatively, choose
- structures manually by selecting with the keyboard and mouse.
+ <li><strong>Selecting Structures</strong><br />You can select
+ the structures to you want to open and view by selecting them with
+ the mouse and keyboard.<br />By default, if structures were
+ discovered, then some will already be selected according to the
+ criteria shown in the drop-down menu. The default criteria is
+ 'highest resolution', simply choose another to pick structures in
+ a different way.<br />
<ul>
<li><strong>Viewing Cached Structures</strong><br />If you
have previously downloaded structures for your sequences, they
<li>If another structure is already shown for the current
alignment, then you will be asked if you want to add and <a
- href="jmol.html#align"
- >align this structure</a> to the structure in the existing view. (<em>new
- feature in Jalview 2.6</em>).
+ href="jmol.html#align">align this structure</a> to the structure
+ in the existing view. (<em>new feature in Jalview 2.6</em>).
</li>
<li>If the structure is already shown, then you will be
<p>
- <strong>Importing PDB Entries or files in PDB format</strong><br>
- You can retrieve sequences from the PDB using the <a
- href="pdbsequencefetcher.html"
- >Sequence Fetcher</a>. Any sequences retrieved with this service are
- automatically associated with their source database entry. For PDB
- sequences, simply select PDB as the database and enter your known
- PDB id (appended with ':' and a chain code, if desired).<br>
- Jalview will also read PDB files directly. Simply load in the file
- as you would an alignment file. The sequences of any protein or
- nucleotide chains will be extracted from the file and viewed in the
- alignment window.
+ <strong>Retrieving sequences from the PDB</strong><br>You can
+ retrieve sequences from the PDB using the <a
+ href="pdbsequencefetcher.html">Sequence Fetcher</a>. The sequences
+ retrieved with this service are derived directly from the PDB 3D
+ structure data, which can be viewed in the same way above. Secondary
+ structure and temperature factor annotation can also be added. <br />
</p>
-
<p>
- <strong>Importing PDB Entries or files in mmCIF format</strong><br>
- <a href="mmcif.html">mmCIF file format</a> provides an alternative means for
- importing 3D structure data from flat file and EMBL-PDBe
- web-service. To enable mmCIF as the default format for
- importing PBD sequences from the PDB sequence fetcher, add or modify the
- property
- <code>DEFAULT_STRUCTURE_FORMAT=mmCIF</code> in Jalview properties file.
- Once this is done, the steps followed in retrieving PDB format files above can
- be followed to obtain the same data with mmCIF. <em>mmCIF format file support was added in Jalview 2.9.1.</em></p>
-
-
+ <strong>Retrieving sequences from the PDB</strong><br>Jalview
+ will also read PDB files directly - either in PDB format, or <a
+ href="mmcif.html">mmCIF</a>. Simply load in the file as you would
+ an alignment file. The sequences of any protein or nucleotide chains
+ will be extracted from the file and viewed in the alignment window.
+ </p>
<p>
<strong>Associating a large number of PDB files to
desktop, Jalview will give you the option of associating PDB files
with sequences that have the same filename. This means, for example,
you can automatically associate PDB files with names like '1gaq.pdb'
- with sequences that have an ID like '1gaq'. <br />
- <em>Note: This feature was added in Jalview 2.7</em>
+ with sequences that have an ID like '1gaq'. <br /> <em>Note:
+ This feature was added in Jalview 2.7</em>
</p>
<p>
<em>Note for Jalview applet users:<br> Due to the applet
Features"</strong> menu item and the <a href="featuresettings.html">Feature
Settings dialog box</a>.
</p>
+ <br/>
+ <hr>
+ <p>
+ <strong>Switching between mmCIF and PDB format for
+ downloading files from the PDB</strong><br /> Jalview now employs the <a
+ href="mmcif.html">mmCIF format</a> for importing 3D structure data
+ from flat file and EMBL-PDBe web-service, as recommended by the
+ wwwPDB. If you prefer (for any reason) to download data as PDB files
+ instead, then first close Jalview, and add the following line to
+ your .jalview_properties file:<br />
+ <code> DEFAULT_STRUCTURE_FORMAT=PDB </code>
+ <br /> When this setting is configured, Jalview will only request
+ PDB format files from EMBL-EBI's PDBe.<br /> <em>mmCIF format
+ file support was added in Jalview 2.10.</em>
+ </p>
<p>
<em><strong>Outstanding problem with cut'n'pasted
- files in Jalview 2.6 and Jalview 2.7</strong><br> Structures
- imported via the cut'n'paste dialog box will not be correctly
- highlighted or coloured when they are displayed in structure
- views, especially if they contain more than one PDB structure. See
- the bug report at http://issues.jalview.org/browse/JAL-623 for
- news on this problem.</em>
+ files in Jalview 2.6 and Jalview 2.7</strong><br>Structures imported
+ via the cut'n'paste dialog box will not be correctly highlighted
+ or coloured when they are displayed in structure views, especially
+ if they contain more than one PDB structure. See the bug report at
+ http://issues.jalview.org/browse/JAL-623 for news on this problem.</em>
</p>
+
</body>
</html>
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows
a dialog window in which you can retrieve known ids from
- Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
+ UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
Web Services provided by the European Bioinformatics
Institute. See <a href="../features/seqfetch.html">Sequence
Fetcher</a>
</p>
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows a
- dialog window in which you can select known ids from Uniprot,
+ dialog window in which you can select known ids from UniProt,
EMBL, EMBLCDS, PDB, PFAM, or RFAM databases using Web Services
provided by the European Bioinformatics Institute. See <a
href="../features/seqfetch.html"
</ul></li>
<li><strong>Fetch Sequence<br>
</strong><em>Shows a dialog window in which you can select known ids
- from Uniprot, EMBL, EMBLCDS or PDB database using Web
+ from UniProt, EMBL, EMBLCDS or PDB database using Web
Services provided by the European Bioinformatics Institute.</em></li>
<li><strong>Save Project</strong><br> <em>Saves
all currently open alignment windows with their current view
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>13/9/2016</em></strong>
</div>
</td>
<td><em>General</em>
</ul> <em>Application</em>
<ul>
<li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
<li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
<li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
<li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
<a href="https://www.certum.eu">Certum</a> to the Jalview
open source project).
</li>
- <li>Jalview SRS links replaced by Uniprot and EBI-search
+ <li>Jalview SRS links replaced by UniProt and EBI-search
</li>
<li>Output in Stockholm format</li>
<li>Allow import of data from gzipped files</li>
current built in colourscheme is saved as new scheme</li>
<li>AlignFrame->Save in application pops up save
dialog for valid filename/format</li>
- <li>Cannot view associated structure for Uniprot sequence</li>
- <li>PDB file association breaks for Uniprot sequence
+ <li>Cannot view associated structure for UniProt sequence</li>
+ <li>PDB file association breaks for UniProt sequence
P37173</li>
<li>Associate PDB from file dialog does not tell you
which sequence is to be associated with the file</li>
<li>Save works when Jalview project is default format</li>
<li>Save as dialog opened if current alignment format is
not a valid output format</li>
- <li>Uniprot canonical names introduced for both das and
+ <li>UniProt canonical names introduced for both das and
vamsas</li>
<li>Histidine should be midblue (not pink!) in Zappo</li>
<li>error messages passed up and output when data read
due to null pointer exceptions</li>
<li>Secondary structure lines are drawn starting from
first column of alignment</li>
- <li>Uniprot XML import updated for new schema release in
+ <li>UniProt XML import updated for new schema release in
July 2008</li>
<li>Sequence feature to sequence ID match for Features
file is case-insensitive</li>
<li>Re-instated Zoom function for PCA
<li>Sequence descriptions conserved in web service
analysis results
- <li>Uniprot ID discoverer uses any word separated by
+ <li>UniProt ID discoverer uses any word separated by
∣
<li>WsDbFetch query/result association resolved
<li>Tree leaf to sequence mapping improved
<p>
<strong>The Sequence Identification Process</strong><br> The
method of accession id discovery is derived from the method which
- earlier Jalview versions used for Uniprot sequence feature retrieval,
- and was originally restricted to the identification of valid Uniprot
+ earlier Jalview versions used for UniProt sequence feature retrieval,
+ and was originally restricted to the identification of valid UniProt
accessions.<br> Essentially, Jalview will try to retrieve records
from a subset of the databases accessible by the <a
href="../features/seqfetch.html"
<strong>What's new ?</strong>
</p>
<p>
- Jalview 2.9.1 is the next major release in the Jalview 2.9 series. Full details are in the
- <a href="releases.html#Jalview.2.9.1">Jalview 2.9.1 Release Notes</a>.
+ Jalview 2.10 is the next major release in the Jalview 2 series. Full details are in the
+ <a href="releases.html#Jalview.2.10">Jalview 2.10 Release Notes</a>, but the highlights are below.
</p>
<p>
- <strong>Highlights in Jalview 2.9.1</strong>
+ <strong>Highlights in Jalview 2.10</strong>
<ul>
+ <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes, transcripts and
+ proteins can be retrieved via Jalview's new Ensembl REST client.</li>
+ <li><strong>Improved sequence/structure mappings.</strong>
+ Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) to
+ match PDB data positions in UniProt sequences.</li>
</ul>
</body>
git://source.jalview.org / jalview.git / commitdiff