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