--- /dev/null
+<html>\r
+<head><title>PDB Viewer</title></head>\r
+<body>\r
+<p><strong>Viewing PDB Structures</strong></p>\r
+<p>Jalview has a simple 3D structure viewer which can load PDB files and associate \r
+ the structure with a sequence in an alignment. </p>\r
+<p>There are 2 ways to load and associate a PDB file into Jalview application.</p>\r
+<ul>\r
+ <li>Select "<a href="seqfeatures.html">Sequence Features</a>" from \r
+ the "View" menu. This will attempt to match your sequences with \r
+ the Uniprot database first by name, then by sequence. The same process will \r
+ make note of any PDB files associated with each sequence. </li>\r
+ <li>Select "<a href="seqfetch.html">Fetch Sequence</a>" from an alignment \r
+ window or from the main desktop "File" menu. In the popup window \r
+ which appears, select PDB as the database and enter your known PDB id. If \r
+ you know which chain you wish to retrieve, append the chain id after a colon \r
+ eg 1GAQ:B</li>\r
+</ul>\r
+<p>Note the applet can only load PDB files by copying and pasting the text into \r
+ the popup window which appears when "Show PDB Structure" is selected \r
+ after right clicking on a sequence name.</p>\r
+<p>To see a particular structure, right click on a sequence name and from the \r
+ popup menu select "Sequence -> View PDB Entry". </p>\r
+<p>The PDB Structure viewer will perform a pairwise alignment of your sequence \r
+ and each PDB chain sequence. To view the results of the mapping, select "File \r
+ -> View Mapping" from the structure viewer window. </p>\r
+<p>Moving the mouse over the structure will highlight the residue in the alignment \r
+ window, and vice versa.</p>\r
+<p><em>Tips for Viewing Structures</em></p>\r
+<ul>\r
+ <li>Colour By Sequence follows the exact colours of the alignment window, including \r
+ sequence features. Thus you can easily view Uniprot sequence features, eg \r
+ helix or metal binding sites on both the alignment and structure viewer.</li>\r
+ <li>Deselect Colours->Show All Chains in order to view only the mapped chain. \r
+ </li>\r
+ <li>Use Wireframe, without depthcue, and without Z Buffering in order to accelerate \r
+ the rendering of the structure. </li>\r
+ <li>You can save an image of your structure as a PNG or EPS file.</li>\r
+</ul>\r
+</body>\r
+</html>\r
be opened when Jalview is started. You can change the default file by clicking \r
on file name and either typing in the file path or selecting it from the file \r
chooser window. </p>\r
-<p>The "Connections" tab allows you to change the links made from Jalview \r
- to your default web browser.</p>\r
+<p>The <strong>"Connections"</strong> tab allows you to change the links \r
+ made from Jalview to your default web browser.</p>\r
<p><em>URL Link From Sequence ID</em><br>\r
Right click a sequence id to see a popup menu with "Link" as one of \r
the items. By default the item "SRS" is added to this link menu. This \r
box "Use a Proxy Server" and enter the address and port details as \r
necessary. Web Services will not work if you are using a proxy server and do \r
not enter the settings here.</p>\r
-<p>The "Export" tab has a selection box allowing the user to set a default \r
- rendering style for EPS export. "Lineart" will produce an accurate \r
- representation of the visible alignment in Jalview, all the characters will \r
- be graphics objects. "Text" will produce a much smaller file and will \r
- rely on the software you use to view the EPS file, such as Adobe Illustrator, \r
- having the same font as the file was created with. You will only be able to \r
- edit text in an EPS file if you select the "Text" option.<br>\r
+<p>The "<strong>Output</strong>" tab has a selection box allowing the \r
+ user to set a default rendering style for EPS export. "Lineart" will \r
+ produce an accurate representation of the visible alignment in Jalview, all \r
+ the characters will be graphics objects. "Text" will produce a much \r
+ smaller file and will rely on the software you use to view the EPS file, such \r
+ as Adobe Illustrator, having the same font as the file was created with. You \r
+ will only be able to edit text in an EPS file if you select the "Text" \r
+ option.<br>\r
Choose "Prompt each time" to select between Lineart and Text each \r
time you make an EPS file.</p>\r
+<p>The output tab also has a group of checkboxes for each file format. If these \r
+ are ticked, then Jalview will write files with the start and end sequence positions \r
+ appended to each sequence id. If the boxes are left unchecked for a paritcular \r
+ format, the sequence limits will not be appended to the sequence id. </p>\r
<p> </p>\r
<p> </p>\r
</body>\r
<head><title>Sequence Features</title></head>\r
<body>\r
<p><strong>View→Sequence Features</strong></p>\r
-<p>When this option is selected, sequence features extracted from the\r
- <a href="http://www.ebi.uniprot.org/">Uniprot</a> record for each\r
- sequence are displayed on the alignment.</p>\r
-<p>Currently, sequence features are rendered in red or blue, dependent\r
- upon their type:</p><ul>\r
- <li>Features associated with a particular residue are coloured\r
- red<br><em>e.g. an active site residue</em></li>\r
- <li>Features which span a region are coloured blue<br>\r
-<em>e.g. a region of sequence with known structure</em>\r
-</li>\r
-</ul></p>\r
+<p>When this option is selected, sequence features extracted from the <a href="http://www.ebi.uniprot.org/">Uniprot</a> \r
+ record for each sequence are displayed on the alignment.</p>\r
+<p>Jalview will attempt to retrieve sequence features from Uniprot files using \r
+ the EBI dbFetch web service using the given sequence names. A 100% match with \r
+ the Uniprot record is required to view the Sequence Features. If the match is \r
+ not 100%, Jalview will run EBI web service WUBlast to find unknown sequences. \r
+ You will be asked whether to proceed with this step, as it can take some time, \r
+ especially if the EBI servers are busy. </p>\r
<p>More information about the feature is given in a tooltip, which is\r
viewed by moving the mouse pointer over a sequence feature. The\r
description associated with the feature will then be displayed in a small\r
label near the pointer.</p>\r
-<p>After the Sequence Features option is selected, there may be some delay before\r
- the features are actually rendered, as jalview first determines if\r
- the sequences are contained in Uniprot and then retrieves any sequence\r
- records. This delay will normally only happen once for a particular\r
- set of sequences, as jalview caches uniprot records in a file in your home\r
- directory called '.jalview.uniprot.xml'.\r
-\r
- <p><strong>The Sequence Identification Process</strong>\r
+<p><strong>View→Feature Settings...</strong>\r
+<p>Once sequence features have been loaded onto an alignment features can be hidden \r
+ or have their rendering priority changed using the Feature Settings dialog. \r
+ This displays all the features loaded, the colour and whether to display the \r
+ feature or not. You can easily change the colour by clicking the colour box.<br>\r
+ It is important to realise that the order in which features are drawn to the \r
+ alignment may result in overlapping features being hidden. Features at the foot \r
+ of the table are rendered first. Therefore features higher up the table will \r
+ be drawn over the top of lower featrues. You can change the order of the feature \r
+ priority by dragging the feature with your mouse. <br>\r
+ Use the transparency setting as another way to visualise overlapping features. \r
+<p><strong><em>You can save all features, with their current colours and visibility \r
+ in a Jalview format file. </em></strong>\r
+<p><strong>The Sequence Identification Process</strong>\r
\r
</p>\r
<p>The first step in the procedure for matching uniprot IDs to\r
--- /dev/null
+<html>\r
+<head><title>Sequence Fetcher</title></head>\r
+<body>\r
+<p><strong>Sequence Fetcher</strong></p>\r
+<p>The Sequence Fetcher can be started from the main desktop "File" \r
+ menu or from a particular alignment window.</p>\r
+<p>Select which database to fetch your sequence from and enter the sequence id. \r
+ If you are retrieving sequences from PDB database and you know which chain you \r
+ would like to retrieve, append the chain id after colon to the PDB id. eg 1GAQ:A</p>\r
+<p>The Sequence Fetcher uses WSDBFetch provided by the European Bioinformatics \r
+ Institute. If you use this service please quote:</p>\r
+<p>Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar \r
+ S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R. <br>\r
+ SOAP-based services provided by the European Bioinformatics Institute.<br>\r
+ Nucleic Acids Res. 33(1):W25-W28 (2005) <br>\r
+ <br>\r
+</p>\r
+</body>\r
+</html>\r
-<html>
-<head>
-<title>Exporting alignments as artwork</title>
-</head>
-<body>
-<p><strong>Exporting alignments as graphics and lineart<a name="export"></a></strong></p>
-<p>The alignment view can be printed using
-<strong>File→Print</strong>, or exported in a number of ways via the
-<strong>File→Export</strong> menu:
-<ul>
-<li>HTML<br><em>for viewing in a web browser</em>
-</li>
-<li>PNG - a Portable Networks Graphics image<br><em>For low quality
-diagrams and powerpoint presentations</em>
-</li>
-<li>EPS - an Encapsulated Postscript Document<br><em>For high quality
-diagrams and publications.</em>
-</li></ul>
-
-<p><em>Tips for working with EPS Files</em></p><ul><li>The EPS file generated by jalview contains vector
- graphics which are directly editable in graphics applications such as
- Adobe Illustrator.</li>
-<li>When importing an EPS into to a Microsoft office document, a snapshot image of the
- file will be displayed which often looks blurred. Right-click the
- image and choose "Edit image." to convert it to word
- drawing objects which give a truer WYSIWIG representation.
- </li>
- <li>
- Mac OSX users will find that eps files are automatically converted into
- PDF files.
- </li>
-</p>
-</body>
-</html>
+<html>\r
+<head>\r
+<title>Exporting alignments as artwork</title>\r
+</head>\r
+<body>\r
+<p><strong>Exporting alignments as graphics and lineart<a name="export"></a></strong></p>\r
+<p>The alignment view can be printed using\r
+<strong>File→Print</strong>, or exported in a number of ways via the\r
+<strong>File→Export</strong> menu:\r
+<ul>\r
+<li>HTML<br><em>for viewing in a web browser</em>\r
+</li>\r
+<li>PNG - a Portable Networks Graphics image<br><em>For low quality\r
+diagrams and powerpoint presentations</em>\r
+</li>\r
+<li>EPS - an Encapsulated Postscript Document<br><em>For high quality\r
+diagrams and publications.</em>\r
+</li></ul>\r
+ \r
+<p><em>Tips for working with EPS Files</em></p><li>The EPS file generated by jalview contains vector\r
+ graphics which are directly editable in graphics applications such as\r
+ Adobe Illustrator.</li>\r
+<li>When importing an EPS into to a Microsoft office document, a snapshot image of the\r
+ file will be displayed which often looks blurred. Right-click the\r
+ image and choose "Edit image." to convert it to word\r
+ drawing objects which give a truer WYSIWIG representation.\r
+ </li>\r
+ <li>\r
+ Mac OSX users will find that eps files are automatically converted into\r
+ PDF files. \r
+ </li>\r
+</p>\r
+</body>\r
+</html>\r
<p>Each alignment, whether it is the original or an edited version may be saved\r
in the standard formats using <strong>File→Save As</strong></p>\r
<p><em>Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm</em></p>\r
+Jalview will by default append the sequence start and end to each sequence name, \r
+in the format /start-end. If you do not want this behaviour for a particular file \r
+output, open the "Output" tab on the Preferences window where you can \r
+select which file formats you want to append the start and end sequence positions \r
+for. \r
<p>You can also save the current set of alignments and their colours, annotations and\r
trees in a Jalview archive file using <strong>Desktop→Save project</strong>. </p>\r
<p> </p>\r
<li>Edits can be undone, and redone!</li>\r
</ul>\r
<table border="1">\r
- <tr>\r
+ <tr> \r
<td><div align="center"><em><strong>Release</strong></em></div></td>\r
<td><div align="center"><em><strong>New Features</strong></em></div></td>\r
<td><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
+ <td><div align="center"><strong>2.07</strong><br>\r
+ 7 /12/05</div></td>\r
+ <td><ul>\r
+ <li>PDB Structure Viewer enhanced</li>\r
+ <li>Sequence Feature retrieval and display enhanced</li>\r
+ <li>Choose to output sequence start-end after sequence name for file output</li>\r
+ <li>Sequence Fetcher WSDBFetch@EBI</li>\r
+ </ul></td>\r
+ <td><ul>\r
+ <li>HTML output writes groups and features</li>\r
+ <li>Group editing is Control and mouse click</li>\r
+ <li>Applet can read feature files, PDB files and can be used for HTML \r
+ form input</li>\r
+ </ul></td>\r
+ </tr>\r
+ <tr> \r
<td><div align="center"><strong>2.06</strong><br>\r
28/9/05</div></td>\r
<td><ul>\r
<li>Runs with -nodisplay from command line</li>\r
</ul></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
<td><div align="center"><strong>2.05b</strong><br>\r
15/9/05</div></td>\r
<td><ul>\r
<li>Several GUI bugs resolved</li>\r
</ul></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
<td><div align="center"><strong>2.05</strong><br>\r
30/8/05</div></td>\r
<td><ul>\r
<li>Several GUI bugs resolved</li>\r
</ul></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
<td><div align="center"><strong>2.04</strong><br>\r
24/8/05</div></td>\r
<td><ul>\r
<li>Improved loading of Jalview files</li>\r
</ul></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
<td> <div align="center"><strong>2.03</strong><br>\r
18/8/05</div></td>\r
<td><ul>\r
<li>InstallAnywhere download for Sparc Solaris</li>\r
</ul></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
<td> <div align="center"><strong>2.02</strong><br>\r
18/7/05</div></td>\r
<td> </td>\r
<li>Copy & Paste order of sequences maintains alignment order.</li>\r
</ul></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
<td><div align="center"><strong>2.01</strong><br>\r
12/7/05</div></td>\r
<td><ul>\r
<li>FileChooser sorts columns.</li>\r
<li>Can remove groups one by one.</li>\r
<li>Filechooser icons installed.</li>\r
- <li>Finder ignores return character when searching. Return key will initiate\r
+ <li>Finder ignores return character when searching. Return key will initiate \r
a search.<br>\r
</li>\r
</ul></td>\r
</tr>\r
- <tr>\r
+ <tr> \r
<td> <div align="center"><strong>2.0</strong><br>\r
20/6/05</div></td>\r
<td ><ul>\r
git://source.jalview.org / jalview.git / commitdiff