3 <title>Popup Menu</title>
7 <p><strong>Popup Menu</strong><br>
8 <em>This menu is visible when right clicking either within a
9 selected region on the alignment or on a selected sequence name. It may
10 not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
12 <li><strong>Selection</strong>
14 <li><strong>Edit </strong>
16 <li><strong>Copy</strong><br>
17 <em>Copys the selected region. In the applet version, the copied
18 sequences are not available to the system clipboard.</em></li>
20 </strong><em>Cuts the selected region from the alignment. In the applet
21 version, the copied sequences are not available to the system
23 <li><strong>To Upper Case</strong><em><strong><br>
24 </strong><em>Changes the case of selected region to lower case.</em> </em></li>
25 <li><strong>To Lower Case<br>
26 </strong><em>Changes the case of selected region to upper case.</em><strong>
28 <li><strong>Toggle Case</strong><br>
29 <em>Switches the case of all residues within the selected
33 <li><strong>Output to Textbox<br>
34 </strong><em>The selection area will be output to a a text window in the
35 selected alignment format. </em></li>
36 <li><strong><a href="../features/creatinFeatures.html">Create
37 Sequence Feature...</a></strong><br>
38 <em>Opens the dialog box for creating sequence features over the
39 currently selected region on each selected sequence.</em></li>
40 <li><strong>Group</strong><br>
41 <em>Group Operations</em>
43 <li><strong>Group</strong><em>This will display a window
44 asking for the name of the currently selected group. Click OK to set
45 the name, cancel to use the default group name. </em></li>
46 <li><strong>Remove Group<br>
47 </strong><em>This will undefine the selected group. </em><strong> </strong></li>
48 <li><strong>Group Colour<br>
49 </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a> of
50 the group.</em><strong> </strong></li>
52 </strong><em>If selected the background of a residue within the selected
53 group will be coloured according to the assigned colour scheme.</em><strong>
56 </strong><em>If selected the selected group will display text. </em></li>
57 <li><strong>Colour Text<br>
58 </strong><em>If selected the selected group will display text in a colour
59 slightly darker than the background colour of that residue.</em></li>
60 <li><strong>Border Colour <br>
61 </strong><em>Selecting this will display a "Colour Chooser"
62 window. Select a colour than press OK to set the border colour of a
68 <li><strong>Sequence Id<br>
69 </strong><em>This menu is only visible if you right-click on a sequence
72 <li><strong>Edit Name/Description<br>
73 </strong><em>You may edit the name and description of each sequence. A
74 window will be displayed asking for a new sequence name and sequence
75 description to be entered. Press OK to accept your edit. To save
76 sequence descriptions, you must save in Fasta, PIR or Jalview File
78 <li><strong>Associate Structure with Sequence</strong>
80 <li><strong>From File<br>
81 </strong><em>Load a PDB file from local disk which will be associated
82 with this sequence. This file will be used if the user subsequently
83 clicks on "View PDB Structure" menu item.</em></li>
84 <li><strong>Enter PDB id<br>
85 </strong><em>Enter the PDB id from an input window. This PDB id will be
86 used by the service WSDBFetch, provided by the EBI, to fetch the PDB
87 file if the user subsequently clicks on "View PDB
88 Structure" menu item. </em></li>
89 <li><strong>Discover PDB ids<br>
90 </strong><em>This will use the service WSDBFetch, provided by the EBI, to
91 retrieve all PDB ids associated with the sequences in the alignment
92 if the sequences have valid Uniprot names or accession ids. </em></li>
95 <li><strong>View PDB Structure<br>
96 </strong><em> If the sequence has an associated PDB file added by one of
97 the methods described above, Jalview will display a 3D interactive
98 viewer of the file.<br>
99 This entry is only present if the sequence has an <a
100 href="../features/viewingpdbs.html">associated PDB structure</a>. </em></li>
101 <li><strong>Represent Group With (Sequence Id)</strong><br>
102 <em>All sequences in the current selection group will be hidden,
103 apart from (Sequence Id). Any edits performed on the visible
104 representative sequence will be propagated to the hidden sequences. </em></li>
105 <li><strong>Link</strong><br>
106 <em>This menu item lists all links which have been set up in the
107 <a href="../features/preferences.html">Preferences</a> Connections
108 tab.</em><strong><br>
112 <li><strong>Hide Sequences</strong><br>
113 <em>This menu item lists all links which have been set up in the <a
114 href="../features/preferences.html">Preferences</a> Connections tab.
115 It is only displayed when you right click (Apple click) on a sequence
116 id. </em><strong><br>