<title>PDB Viewing</title>
</head>
<body>
-<p><strong>Viewing PDB Structures</strong></p>
<p>
- Jalview can view protein structures associated with a sequence via the
- <strong>"Structure→"</strong> submenu from a sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>.
+ <strong>Viewing PDB Structures</strong>
</p>
+ Jalview can be used to view protein structures by following the steps below:
+ <ol>
+ <li>Select the <strong>"View Structure"</strong> option from a
+ sequence's <a href="../menus/popupMenu.html">pop-up menu</a>.
+ <ul>
+ <li>If one or more structures exists for the given sequence, the <strong>'Structure Chooser'</strong>
+ dialogue is opened with a list of the found structures meta-data.</li>
+ <li>However, if no structure was found, the <strong>'Structure Chooser'</strong> dialogue is opened with options for manual association of PDB structures.</li>
+ </ul>
+ </li>
+ <li>Choose the structure to view from the presented structures
+ summary list. This can be done either manually by clicking directly
+ on the desired structure from the list, or automatically by
+ using the filter combo-box which enables filtering on certain
+ criteria like quality, resolution, etc. The best structure for the chosen criteria is automatically selected by the filtration process. </li>
+ <li>When the desired structure(s) have been selected, they can be
+ viewed by clicking the <strong>"View"</strong> button below the summary list.
+ </li>
+
+ </ol>
+
The
<a href="jmol.html">Jmol viewer</a> has been included since Jalview
2.3. Jalview 2.8.2 included support for <a href="chimera.html">Chimera</a>, provided it is
href="xsspannotation.html">Annotation from Structure</a> page for
more information.
</p>
- <p>The following menu entries are provided for viewing structure data<br>
+ <!--
+ <p>The following menu entries are provided for viewing structure data
<ul>
<li>The <strong>"Structure→View
Structure→</strong> submenu allows a single PDB structure to be chosen
<em>The View representative structures option was introduced in
Jalview 2.8.1</em></li>
</ul>
-</p>
+</p> -->
-<p>If a single pdb
+<p>If a <strong>single</strong> pdb
structure is selected, one of the following will happen:</p>
<ul>
</a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for more information about the display.</li>
</ul>
<p><strong>Associating PDB files with Sequences</strong></p>
- <p>To associate PDB files with a sequence, right click on a sequence
-ID and select "Structure<strong>→</strong> Associate Structure with
-Sequence", and one of the submenus:</p>
+ <p>Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the <strong>"View Structure"</strong> option is selected
+ from a sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Jalview uses the sequence's ID to query the PDB Rest API, provided by the
+ EBI to discover PDB ids associated with the sequence. </p>
+
+ <p><strong>Manual association of PDB files with Sequences</strong> </p>
+ <p>To manually associate PDB files with a sequence, right click on a sequence
+ID and select the <strong>"View Structure"</strong> option, this opens the <strong>'Structure Chooser'</strong> dialogue. Then pick any of the follwing options listed below from the drop-down menu in the <strong>'Structure Chooser'</strong> panel to proceed with manual association:
<ul>
- <li>From File - You can load a PDB file from the local machine or
+ <li><strong>From File</strong> - You can load a PDB file from the local machine or
network and associate it with the selected sequence. PDB files
associated in this way will also be saved in the <a
href="jalarchive.html">Jalview Archive file</a>.<br>
</li>
-
- <li>Enter PDB Id - Jalview will use WSDBFetch, provided by the
+ <li><strong>Enter PDB Id</strong> - Jalview will use the PDB Rest API, provided by the
EBI, to fetch the PDB file with the entered Id.<br>
</li>
-
- <li>Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the
- EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.</li>
</ul>
+<strong>Note:</strong> The drop-down menu in the 'Structure Chooser' panel may contain other options employed for filtering structures when one or more structures are auto-discovered.
+
<p><strong>Importing PDB Entries or files in PDB format</strong><br>
You can retrieve sequences from the PDB using the <a
href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
</head>
<body>
-<p><strong>Popup Menu</strong><br>
-<em>This menu is visible when right clicking either within a
-selected region on the alignment or on a selected sequence name. It may
-not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
-<ul>
- <li><strong>Selection</strong>
- <ul>
- <li><a name="sqreport"><strong>Sequence Details...<br>
- </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
- and database cross references</a> normally shown in the sequence's
- tooltip.</em></li>
- <li><strong>Show Annotations...<br>
- </strong><em>Choose to show (unhide) either All or
- a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
- <li><strong>Hide Annotations...<br>
- </strong><em>Choose to hide either All or
- a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
- <li><a name="addrefannot"><strong>Add Reference Annotations<br>
- </strong><em>Add to the alignment window any annotations on the selected sequences
- which have been read from reference sources or calculated (for example,
- secondary structure derived from 3D structure). (Since Jalview 2.8.2)</em></li>
- <li><strong>Edit </strong>
- <ul>
- <li><strong>Copy</strong><br>
- <em>Copies the selected region. In the applet version, the copied sequences
- are not available to the system clipboard.</em></li>
- <li><strong>Cut<br>
- </strong><em>Cuts the selected region from the alignment. In the applet
- version, the copied sequences are not available to the system clipboard.</em></li>
- <li><strong>Edit Sequence</strong><br>
- <em>Edit the selected sequence(s) directly. Spaces will be converted
- to the current gap character.</em></li>
- <li><strong>To Upper Case</strong><em><strong><br>
- </strong><em>Changes the case of selected region to lower case.</em>
- </em></li>
- <li><strong>To Lower Case<br>
- </strong><em>Changes the case of selected region to upper case.</em><strong>
- </strong></li>
- <li><strong>Toggle Case</strong><br>
- <em>Switches the case of all residues within the selected region.</em></li>
- </ul>
- </li>
- <li><strong>Output to Textbox<br>
- </strong><em>The selection area will be output to a a text window in the
- selected alignment format. </em></li>
- <li><strong><a href="../features/creatinFeatures.html">Create Sequence Feature...</a></strong><br>
- <em>Opens the dialog box for creating sequence features over the currently
- selected region on each selected sequence.</em></li>
- <li><strong>Create Group<br>
- </strong><em>This will define a new group from the current selection.</em><strong>
- </strong></li>
- <li><strong>Remove Group<br>
- </strong><em>This will undefine the selected group. </em><strong>
- </strong></li>
- <li><strong>Edit (New) Group</strong><br>
- <em>Group Editing Menu</em> <br />Options in this menu modify
- the name and display properties of the currently selected group, or
- a new group defined using the current selection.
+ <p>
+ <strong>Popup Menu</strong><br> <em>This menu is visible
+ when right clicking either within a selected region on the alignment
+ or on a selected sequence name. It may not be accessible when in
+ 'Cursor Mode' (toggled with the F2 key).</em>
+ </p>
+ <ul>
+ <li><strong>Selection</strong>
+ <ul>
+ <li><a name="sqreport"><strong>Sequence Details...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+ href="../io/exportseqreport.html">HTML report containing the
+ annotation and database cross references</a> normally shown in
+ the sequence's tooltip.
+ </em></li>
+ <li><strong>Show Annotations...<br>
+ </strong><em>Choose to show (unhide) either All or a selected type of
+ annotation for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><strong>Hide Annotations...<br>
+ </strong><em>Choose to hide either All or a selected type of annotation
+ for the selected sequences. (Since Jalview 2.8.2)</em></li>
+ <li><a name="addrefannot"><strong>Add Reference
+ Annotations<br>
+ </strong><em>Add to the alignment window any annotations on the
+ selected sequences which have been read from reference sources or
+ calculated (for example, secondary structure derived from 3D
+ structure). (Since Jalview 2.8.2)</em></li>
+ <li><strong>Edit </strong>
<ul>
- <li><strong>Name: <Group></strong> or <strong>Edit name and description</strong><br><em>The first entry in the
- menu displays the name for the currently selected group, if it has one. Selecting this option opens a window allowing the name and
- description for this group to be edited. Click OK to set the
- new name and decription, and cancel to leave the existing
- name and description unchanged.</em></li>
- <li><strong>Group Colour<br>
- </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
- of the group.</em><strong> </strong></li>
- <li><strong>Boxes<br>
- </strong><em>If selected the background of a residue within the selected
- group will be coloured according to the assigned colour scheme.</em><strong>
- </strong></li>
- <li><strong>Text<br>
- </strong><em>If selected the selected group will display text. </em></li>
- <li><strong>Colour Text<br>
- </strong><em>If selected the selected group will display text in a
- colour slightly darker than the background colour of that residue.</em></li>
- <li><strong>Border Colour <br>
- </strong><em>Selecting this will display a "Colour Chooser"
- window. Select a colour than press OK to set the border colour of
- a group.</em></li>
- <li><strong>Show Unconserved<br>
- </strong><em>When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
- </em></li>
- </ul>
- </li>
-<!-- not available in 2.5 yet
- <li><strong>Group Links<br>
- </strong><em>This menu is only visible if there are group links available for the current selection.
- </em>
- <ul>
- <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
- <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
- <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
- </ul>
- <em>Group Links were added in Jalview 2.5</em></li>
---> </ul>
- </li>
- <li><strong>Sequence Id<br>
- </strong><em>This menu is only visible if you right-click on a sequence name.
- </em>
- <ul>
- <li><a name="sqreport"><strong>Sequence Details ...<br>
- </strong></a><em>(Since Jalview 2.8)<br>Open an <a href="../io/exportseqreport.html">HTML report containing the annotation
- and database cross references</a> normally shown in the sequence's
- tooltip.</em></li>
- <li><strong>Edit Name/Description<br>
- </strong><em>You may edit the name and description of each sequence. A
- window will be displayed asking for a new sequence name and sequence description
- to be entered. Press OK to accept your edit. To save sequence descriptions,
- you must save in Fasta, PIR or Jalview File format.</em></li>
- <li><a href="sqaddrefannot"><strong>Add Reference Annotations<br></strong><em>When enabled, copies any available alignment annotation for this sequence to the current view.</em></li>
- <li><strong>Represent Group With (Sequence Id)</strong><br>
- <em>All sequences in the current selection group will be hidden, apart
- from (Sequence Id). Any edits performed on the visible representative
- sequence will be propagated to the hidden sequences. </em></li>
- <li><a name="sqid.popup"><strong>Link</strong><br>
- <em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a>
- Connections tab.<br>
- Since Jalview 2.4, links will also be made for database cross
- references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
- <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to
- the sequence, and any regular-expression based URL links that
- matched the description line.
- </em><strong><br>
- </strong></li>
- </ul>
- </li>
- <li><strong>Structure</strong>
- </strong><em>This menu is only visible if you right-click on a sequence name.
- </em>
- <ul>
- <li><strong>Associate Structure with Sequence</strong>
+ <li><strong>Copy</strong><br> <em>Copies the
+ selected region. In the applet version, the copied sequences are
+ not available to the system clipboard.</em></li>
+ <li><strong>Cut<br>
+ </strong><em>Cuts the selected region from the alignment. In the
+ applet version, the copied sequences are not available to the
+ system clipboard.</em></li>
+ <li><strong>Edit Sequence</strong><br> <em>Edit the
+ selected sequence(s) directly. Spaces will be converted to the
+ current gap character.</em></li>
+ <li><strong>To Upper Case</strong><em><strong><br>
+ </strong><em>Changes the case of selected region to lower case.</em> </em></li>
+ <li><strong>To Lower Case<br>
+ </strong><em>Changes the case of selected region to upper case.</em><strong>
+ </strong></li>
+ <li><strong>Toggle Case</strong><br> <em>Switches
+ the case of all residues within the selected region.</em></li>
+ </ul></li>
+ <li><strong>Output to Textbox<br>
+ </strong><em>The selection area will be output to a a text window in the
+ selected alignment format. </em></li>
+ <li><strong><a href="../features/creatinFeatures.html">Create
+ Sequence Feature...</a></strong><br> <em>Opens the dialog box for
+ creating sequence features over the currently selected region on
+ each selected sequence.</em></li>
+ <li><strong>Create Group<br>
+ </strong><em>This will define a new group from the current selection.</em><strong>
+ </strong></li>
+ <li><strong>Remove Group<br>
+ </strong><em>This will undefine the selected group. </em><strong> </strong></li>
+ <li><strong>Edit (New) Group</strong><br> <em>Group
+ Editing Menu</em> <br />Options in this menu modify the name and
+ display properties of the currently selected group, or a new group
+ defined using the current selection.
+ <ul>
+ <li><strong>Name: <Group></strong> or <strong>Edit
+ name and description</strong><br> <em>The first entry in the
+ menu displays the name for the currently selected group, if it
+ has one. Selecting this option opens a window allowing the name
+ and description for this group to be edited. Click OK to set the
+ new name and decription, and cancel to leave the existing name
+ and description unchanged.</em></li>
+ <li><strong>Group Colour<br>
+ </strong><em>Sets the <a href="../colourSchemes/index.html">colour</a>
+ of the group.
+ </em><strong> </strong></li>
+ <li><strong>Boxes<br>
+ </strong><em>If selected the background of a residue within the
+ selected group will be coloured according to the assigned colour
+ scheme.</em><strong> </strong></li>
+ <li><strong>Text<br>
+ </strong><em>If selected the selected group will display text. </em></li>
+ <li><strong>Colour Text<br>
+ </strong><em>If selected the selected group will display text in a
+ colour slightly darker than the background colour of that
+ residue.</em></li>
+ <li><strong>Border Colour <br>
+ </strong><em>Selecting this will display a "Colour Chooser"
+ window. Select a colour than press OK to set the border colour
+ of a group.</em></li>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all symbols in the group matching
+ the consensus sequence at that column will be rendered as a '.',
+ highlighting mutations in the group area. </em></li>
+ </ul></li>
+
+ </ul></li>
+ <li><strong>Sequence Id<br>
+ </strong><em>This menu is only visible if you right-click on a sequence
+ name. </em>
+ <ul>
+ <li><a name="sqreport"><strong>Sequence Details
+ ...<br>
+ </strong></a><em>(Since Jalview 2.8)<br>Open an <a
+ href="../io/exportseqreport.html">HTML report containing the
+ annotation and database cross references</a> normally shown in the
+ sequence's tooltip.
+ </em></li>
+ <li><strong>Edit Name/Description<br>
+ </strong><em>You may edit the name and description of each sequence. A
+ window will be displayed asking for a new sequence name and
+ sequence description to be entered. Press OK to accept your edit.
+ To save sequence descriptions, you must save in Fasta, PIR or
+ Jalview File format.</em></li>
+ <li><a href="sqaddrefannot"><strong>Add Reference
+ Annotations<br>
+ </strong><em>When enabled, copies any available alignment annotation
+ for this sequence to the current view.</em></li>
+ <li><strong>Represent Group With (Sequence Id)</strong><br>
+ <em>All sequences in the current selection group will be
+ hidden, apart from (Sequence Id). Any edits performed on the
+ visible representative sequence will be propagated to the hidden
+ sequences. </em></li>
+ <li><a name="sqid.popup"><strong>Link</strong><br> <em>This
+ menu item lists all links which have been set up in the <a
+ href="../features/preferences.html">Preferences</a> Connections
+ tab.<br> Since Jalview 2.4, links will also be made for
+ database cross references (where the database name exactly
+ matches the link name set up in <a
+ href="../features/preferences.html">Preferences</a>). <br>Since
+ Jalview 2.5, links are also shown for non-positional sequence
+ features attached to the sequence, and any regular-expression
+ based URL links that matched the description line.
+ </em><strong><br> </strong></li>
+ </ul></li>
+ <li><strong>View Structure</strong> </strong><em>This menu is only
+ visible if you right-click on a sequence name. If the
+ sequence has an associated PDB file(s), Jalview will open a 'Structure Chooser'
+ dialogue with options to select the structure which will eventually be opened in
+ a 3D interactive view.<br> These entries will only be present if the sequence
+ has <a href="../features/viewingpdbs.html">associated PDB
+ structures</a>.<br /> If the sequence or alignment has RNA structure,
+ then <strong>2D RNA</strong> entries will also be present enabling
+ you to open a linked view of the RNA structure in <a
+ href="../features/varna.html">VARNA</a>.
+ </em>
+ </li>
+<!--
+ <p>
+ <em>Other menu entries may also be shown if the current
+ selection includes sequences with associated structure data:</em><br>
+ <ul>
+ <li><strong>Associate Structure with Sequence</strong>
<ul>
<li><strong>From File<br>
</strong><em>Load a PDB file from local disk which will be associated
alignment if the sequences have valid Uniprot names or accession ids.
</em></li>
</ul>
- </li>
- <li><strong>View Structure<br>
- </strong><em> If the sequence has an associated PDB file added by one
- of the methods described above, Jalview will open a 3D interactive
- view of the file.<br>
- These entries will only be present if the sequence has <a
- href="../features/viewingpdbs.html">associated PDB structures</a>.<br/>
- If the sequence or alignment has RNA structure, then <strong>2D RNA</strong> entries will also be present enabling you to open a linked view of the RNA structure in <a href="../features/varna.html">VARNA</a>.</em><br>
- </li>
- <p><em>Other menu entries may also be shown if the current selection includes sequences with associated structure data:</em><br>
- <ul>
- <li><strong>"Structure→View all <em>N</em>
- structures<br/>
- </strong><em>Opens a new window containing all structures associated
- with the current selection, superposed according to the currently selected region of the alignment.<br/>(This
- capability was added in Jalview 2.7)</em>
- </li>
- <li><strong>"Structure→View all <em>N</em>
- representative structures<br/>
- </strong><em>Open a new window containing exactly one structure per
- currently selected sequence.<br />
- (The View representative structures option was introduced in
- Jalview 2.8.1)</em></li>
- </ul>
- <br>
- </ul>
- </li>
- <li><strong>Hide Sequences</strong><br>
- <em>Hides the currently selected sequences in this alignment view.</em><strong><br>
- <br>
- </strong></li>
-</ul>
+ </li>
+
+ <ul>
+ <li><strong>Structure→View all <em>N</em>
+ structures<br />
+ </strong><em>Opens a new window containing all structures associated
+ with the current selection, superposed according to the currently
+ selected region of the alignment.<br />(This capability was
+ added in Jalview 2.7)
+ </em></li>
+ <li><strong>Structure→View all <em>N</em>
+ representative structures<br />
+ </strong><em>Open a new window containing exactly one structure per
+ currently selected sequence.<br /> (The View representative
+ structures option was introduced in Jalview 2.8.1)
+ </em></li>
+ </ul>
+ <br> -->
+
+ <li><strong>Hide Sequences</strong><br> <em>Hides the
+ currently selected sequences in this alignment view.</em><strong><br>
+ </strong></li>
+ </ul>
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff