<html>\r
<head><title>Hidden Regions</title></head>\r
<body>\r
-Now you see them, now you dont \r
+<p><strong>Hidden Regions</strong> </p>\r
+<p>To <strong>hide selected sequences </strong>from an alignment, use the "View \r
+ -> Hide -> Selected Sequences" menu item or simply select "Hide \r
+ Sequences" from the Popup menu after a right click on the sequence Ids. \r
+</p>\r
+<p>Hidden sequences will not be used in any calculations, editing or web service \r
+ alignments performed on visible sequences. </p>\r
+<p>A more advanced hide involves a right-mouse click on a sequence, then selecting \r
+ "SequenceID -> Represent Group with SequenceId". Using this method \r
+ of hiding sequences, any edits performed on the visible group representative \r
+ will be propogated to all the sequences in that group. <br>\r
+ The hidden sequences will not be used in any calculations or web service alignments. \r
+</p>\r
+<p> </p>\r
+<p>To <strong>hide selected columns</strong> from an alignment, use the "View \r
+ -> Hide -> Selected Columns" menu item, or right click within a region \r
+ of selected columns in the scale above the alignment (only available in non \r
+ wrapped mode) and select "Hide Columns". </p>\r
+<p>Hidden columns will not be used in any calculations. This allows you to eg. \r
+ create trees from the visible alignment and ignore any poorly aligned sections \r
+ of the alignment, without cutting and deleting them permanently from your alignment.<br>\r
+ It is possible to retrieve the input data to any trees, PCA analysis windows \r
+ which were created from alignments containing hidden columns by using the "File \r
+ -> Input Data..." menu item from the tree window. </p>\r
+<p> Editing the alignment is bound by the hidden columns, ie you cannot move residues \r
+ across a hidden column boundary.</p>\r
+<p>Any web service alignments performed on sequences which contain hidden columns \r
+ send the alignment as a series of chunks delimited by the hidden columns. </p>\r
+<p> </p>\r
+<p> </p>\r
+<p> </p>\r
</body>\r
</html>\r
accessed via the <strong>"Sequence→View PDB\r
entry:"</strong> entry from the sequence's <a\r
href="../menus/popupMenu.html">pop-up menu</a>.</p>\r
-<p>There are two ways to associate PDB files with sequences:</p>\r
+<p>To associate PDB files with a sequence, right click on a sequence ID and select \r
+ "Associate Structure with Sequence", and one of the submenus:</p>\r
<ul>\r
- <li>Select "<a href="seqfeatures.html">Sequence Features</a>" from\r
- the "View" menu, which retrieves any uniprot sequence\r
- records associated with the sequences in the alignment. If, for a\r
- particular sequence's uniprot record there\r
- are any cross-references to PDB structures, then these will be\r
- added to its list of associated database ids.</li>\r
- <li>Retrieve sequences from the PDB using the <a\r
- href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved\r
- with this service are automatically associated with their source\r
- database entry. For PDB sequences, simply select PDB as the database\r
- and enter your known PDB id (appended with ':' and a chain code, if\r
- desired).</li>\r
+ <li>From File - You can load a PDB file from the local machine or network and \r
+ associate it with the selected sequence. PDB files associated in this way \r
+ can be saved in the Jalview Archive file. <br>\r
+ </li>\r
+ <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch \r
+ the PDB file with the entered Id.<br>\r
+ </li>\r
+ <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover \r
+ PDB ids for all the sequences in the alignment which have valid Uniprot names \r
+ / accession ids. </li>\r
</ul>\r
-For help on viewing and colouring structures see the <a\r
-href="pdbviewer.html">PDB Viewer</a> help page.\r
-</p>\r
+<p><strong>Note:</strong> You can retrieve sequences from the PDB using the <a\r
+ href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with this \r
+ service are automatically associated with their source database entry. For PDB \r
+ sequences, simply select PDB as the database and enter your known PDB id (appended \r
+ with ':' and a chain code, if desired).</p>\r
+<p>For help on viewing and colouring structures see the <a\r
+href="pdbviewer.html">PDB Viewer</a> help page. </p> </p>\r
</body>\r
</html>\r
\r
<body>\r
<p><strong>Alignment Window Calculate Menu</strong></p>\r
-<strong>Calculate</strong> \r
<ul>\r
<li><strong>Sort </strong> \r
<ul>\r
\r
<body>\r
<p><strong>Alignment Window Edit Menu</strong></p>\r
-<strong>Edit</strong> \r
<ul>\r
<li><strong>Undo</strong><em><br>\r
This will undo any edits you make to the alignment. This applies to insertion \r
<p>Export Annotations and Features</p>\r
<p>GFF file reading / writing</p>\r
<p>Associate structures with sequences from local PDB files</p>\r
-<p>Add sequences to exisiting alignment</p>\r
+<p>Add sequences to existing alignment</p>\r
<p>Recently opened files / URL lists</p>\r
<p>Applet can launch the full application</p>\r
<p>Applet has transparency for features (Java 1.2 required)</p>\r
git://source.jalview.org / jalview.git / commitdiff