* PURPOSE. See the GNU General Public License for more details.\r
* \r
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
--->
+-->\r
<head>\r
<title>The Jmol PDB Viewer</title>\r
</head>\r
<body>\r
-<p><strong>The Jmol PDB Viewer</strong>\r
-<p>The interactive structure viewing window is opened by selecting\r
-the <strong>"Sequence→View PDB entry:"</strong> entry in\r
-the <a href="../menus/popupMenu.html">sequence id pop-up menu</a>. This\r
-can only be done for sequences which have an <a href="viewingpdbs.html">associated\r
-PDB structure</a>.\r
+<p><strong>The Jmol PDB Viewer</strong></p>\r
<p>Since Jalview 2.3, <a href="http://jmol.sourceforge.net/">Jmol</a>\r
-has been integrated into Jalview. It is automatically used by the\r
-application, and should also run in the applet in all latest web\r
-browsers. If jmol is not available, then the original <a\r
-href="pdbviewer.html">internal pdb viewer</a> will be used as a fallback.\r
+has been integrated into Jalview for interactively viewing structures\r
+opened by selecting the <strong>"Sequence→View PDB\r
+entry:"</strong> option in the <a href="../menus/popupMenu.html">sequence\r
+id pop-up menu</a> (if you can't see this, then you need to <a\r
+ href="viewingpdbs.html">associate a PDB structure</a> with the\r
+sequence). Jmol is available from the Jalview desktop and should also\r
+run in the JalviewLite applet, providing the browser supports Java 1.5.\r
+If Jmol is not available, then the original <a href="pdbviewer.html">internal\r
+pdb viewer</a> will be used as a fallback.</p>\r
+<p><a name="align"><strong>Superposing structures based\r
+on their aligned sequences</strong></a><br>\r
+If several structures are available on the alignment, you may add\r
+additional structures to an existing Jmol view by selecting their entry\r
+in the appropriate pop-up menu. Jalview will ask you if you wish to add\r
+the structure to the existing alignment, and if you do, it will import\r
+and superimpose the new PDB file using the corresponding positions from\r
+the alignment. If the alignment is subsequently edited, you can use the\r
+<a href="#sAlign"><em>Jmol→Align</em></a> menu option from the\r
+menu bar of the structure view window to superpose the structures using\r
+the updated alignment.<br>\r
+<em>Sequence based structure superposition was added in Jalview 2.6</em>\r
</p>\r
-<p><strong>Controls</strong></p>\r
-<p>The structure is by default rendered as a ribbon diagram. Moving the\r
-mouse over the structure brings up tooltips giving the residue name,\r
-PDB residue number and chain code, atom name and number\r
+<p><strong>Controls</strong><br>\r
+The structure is by default rendered as a ribbon diagram. Moving the\r
+mouse over the structure brings up tooltips giving the residue name, PDB\r
+residue number and chain code, atom name and number\r
([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue\r
-in any associated sequences, then this will be highlighted in each\r
-one's alignment window. The converse also occurs - moving the mouse\r
-over an associated residue in an alignment window highlights the associated\r
+in any associated sequences, then this will be highlighted in each one's\r
+alignment window. The converse also occurs - moving the mouse over an\r
+associated residue in an alignment window highlights the associated\r
atoms in the displayed structures.</p>\r
<p>Selecting a residue highlights its associated sequence residue\r
and alpha carbon location. Double clicking an atom allows distances to\r
</tr>\r
<tr>\r
<td>Zoom</td>\r
- <td>Shift + Left Click<br>drag mouse up or down</td>\r
- <td>Shift + Left Click<br>or middle button<br>drag\r
- mouse up or down</td>\r
+ <td>Shift + Left Click<br>\r
+ drag mouse up or down</td>\r
+ <td>Shift + Left Click<br>\r
+ or middle button<br>\r
+ drag mouse up or down</td>\r
<td>Left-Alt + Click and drag mouse up or down</td>\r
</tr>\r
<tr>\r
</tr>\r
<tr>\r
<td>Roll View</td>\r
- <td>Shift + Left Click<br>drag mouse to left or\r
- right</td>\r
- <td>Shift + Left Click<br>or middle button<br>drag mouse to left or right</td>\r
+ <td>Shift + Left Click<br>\r
+ drag mouse to left or right</td>\r
+ <td>Shift + Left Click<br>\r
+ or middle button<br>\r
+ drag mouse to left or right</td>\r
<td>Left-Alt + Click and drag mouse to left or right</td>\r
</tr>\r
<tr>\r
<td>Move Origin</td>\r
- <td>Shift+Control+Left Click<br>or Middle Button<br>\r
+ <td>Shift+Control+Left Click<br>\r
+ or Middle Button<br>\r
+ Drag</td>\r
- <td>Middle-Button<br>and<br>drag</td>\r
- <td>Shift+Control+Left Click<br>or Middle Button<br>\r
+ <td>Middle-Button<br>\r
+ and<br>\r
+ drag</td>\r
+ <td>Shift+Control+Left Click<br>\r
+ or Middle Button<br>\r
and drag</td>\r
</tr>\r
<tr>\r
</tr>\r
</table>\r
</p>\r
-<p>The window has four menus:\r
+<p>The window has up to five menus:\r
<ul>\r
<li><Strong>File<br>\r
</strong>\r
<ul>\r
<li><strong>Save As<br>\r
- </strong><em>Save the displayed PDB File, or the current view as an EPS or PNG file.</em></li>\r
+ </strong><em>Save the displayed PDB File, or the current view as an EPS or\r
+ PNG file.</em></li>\r
<li><strong>View Mapping<br>\r
</strong><em> Opens a text window showing the alignment between the\r
residues corresponding to alpha-carbon atoms in the PDB structure and\r
</li>\r
<li><strong>View</strong>\r
<ul>\r
- <li><strong>Show Chains<br></strong><em>Select which of the PDB\r
- file's chains are to be displayed.</em>\r
- </li>\r
+ <li><strong>Show Chains<br>\r
+ </strong><em>Select which of the PDB file's chains are to be displayed.</em></li>\r
</ul>\r
<li><strong>Colours<br>\r
</strong>\r
residues in blue.</em></li>\r
<li><strong>Standard and User Defined Jalview\r
colourschemes.<br>\r
- </strong><em>The remaining entries apply the colourschemes available from the\r
- standard and user defined <a href="../colourSchemes/index.html">amino\r
+ </strong><em>The remaining entries apply the colourschemes available from\r
+ the standard and user defined <a href="../colourSchemes/index.html">amino\r
acid colours</a>.</em></li>\r
</ul>\r
</li>\r
- <li><strong>Help<br></strong><ul><li><strong>Jmol Help<br></strong><em>Access the Jmol Help\r
- documentation in a new browser window.</em>\r
+ <li><strong>Jmol<br>\r
+ </strong><em>This pulldown menu is only displayed if there are multiple\r
+ structures shown in the Jmol window, and Jalview can also locate at\r
+ least two of the structures in the currently associated alignment view.</em>\r
+ <ul>\r
+ <li><strong><a name="sAlign">Align</a> <br>\r
+ </strong><em> When selected, the associated alignment will be used to\r
+ superimpose all the structures in the view onto the first structure in\r
+ the alignment. The regions used to calculate the superposition will be\r
+ highlighted using the 'Cartoon' rendering style, and the remaining\r
+ data shown as a chain trace.<br>\r
+ (This option was introduced in Jalview 2.6)</em></li>\r
+ </ul>\r
</li>\r
+ <li><strong>Help<br>\r
+ </strong>\r
+ <ul>\r
+ <li><strong>Jmol Help<br>\r
+ </strong><em>Access the Jmol Help documentation in a new browser window.</em></li>\r
</ul>\r
-</li></ul>\r
+ </li>\r
+</ul>\r
</p>\r
-<p><strong>Functionality provided by Jmol</strong>\r
-</p><p>The Jmol menu provides access to a number of features for\r
+<p><strong>Functionality provided by Jmol</strong></p>\r
+<p>Jmol's own functions are accessed by clicking the 'Jmol' logo or\r
+right-clicking in the structure display area. Either way will open the\r
+Jmol pop-up menu, which provides access to a number of features for\r
controlling the colour and display of molecules, adding measurements and\r
-labels, plotting surfaces, and display animation. The 'Set Picking'\r
-menu controls the behaviour of single and double mouse clicking on the\r
-structure.</p>\r
+labels, plotting surfaces, and display animation. The 'Set Picking' menu\r
+controls the behaviour of single and double mouse clicking on the\r
+structure, and the 'Console' option opens the Jmol scripting console.</p>\r
<p>The state of each Jmol display is stored within <a\r
-href="jalarchive.html">jalview archives</a> as a jmol state recovery script\r
-file. This means that any Jmol visualization effects that\r
-you add beyond those provided by Jalview will be able to be stored and\r
-recovered along with the displayed alignments in Jalview.\r
-</p><p><strong>More Information</strong>\r
-</p><p>Jmol is a sophisticated program in its own right, with its own\r
+ href="jalarchive.html">jalview archives</a> as a Jmol state recovery\r
+script file. This means that any Jmol visualization effects that you add\r
+beyond those provided by Jalview will be able to be stored and recovered\r
+along with the displayed alignments in Jalview.</p>\r
+<p><strong>More Information</strong></p>\r
+<p>Jmol is a sophisticated program in its own right, with its own\r
command console and scripting language. Only the essentials have been\r
-described here - the interested reader is referred to \r
-<a href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive\r
-online documenation</a>.</p></p>\r
+described here - the interested reader is referred to <a\r
+ href="http://jmol.sourceforge.net/docs/">Jmol's own comprehensive\r
+online documentation</a>.</p>\r
+</p>\r
</body>\r
</html>\r
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
-<head><title>PDB Viewing</title></head>
+<head>
+<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→View
- PDB entry:"</strong> entries from a sequence's <a
- href="../menus/popupMenu.html">pop-up menu</a>. This will open an
- interactive display of the structure in a new window, or prompt you
- to associate the sequence with an existing view of the selected
- structure. See the <a href="jmol.html">Jmol PDB viewer</a> help page
- for more information about the display.
-</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>Jalview can view protein structures associated with a sequence
+via the <strong>"Structure→View PDB entry:"</strong> entries from a
+sequence's <a href="../menus/popupMenu.html">pop-up menu</a>. Once a pdb
+structure is selected, one of the following will happen:</p>
+
<ul>
- <li>From File - 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 EBI, to fetch
- the PDB file with the entered Id.<br>
- </li>
- <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover
- PDB ids for all the sequences in the alignment which have valid Uniprot names
- / accession ids. </li>
+ <li>If no structures are open, then an interactive display of the
+ structure will be opened in a new window</li>
+
+ <li>If another structure is already shown for the current
+ alignment, then you will be asked if you want to add and <a
+ href="jmol.html#align">align this structure</a> to the structure in
+ the existing view. (<em>new feature in Jalview 2.6</em>)</li>
+
+ <li>If the structure is already shown, then you will be prompted
+ to associate the sequence with an existing view of the selected
+ structure.</li>
+
+ <li style="list-style: none">See the <a href="jmol.html">Jmol
+ PDB viewer</a> help page for more information about the display.</li>
</ul>
+
+
+<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>
+
+<ul>
+ <li>From File - 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
+ EBI, to fetch the PDB file with the entered Id.<br>
+ </li>
+
+ <li>Discover PDB Ids - Jalview uses WSDBFetch, provided by the
+ EBI, to discover PDB ids for all the sequences in the alignment which
+ have valid Uniprot names / accession ids.</li>
+</ul>
+
<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 this
- service are automatically associated with their source database entry. For PDB
- sequences, simply select PDB as the database and enter your known PDB id (appended
- with ':' and a chain code, if desired).
-<br>Jalview will also read PDB files directly. Simply load in the file
-as you would an alignment file. The sequences of any peptide chains
-will be extracted from the file and viewed in the alignment window.
-<br><em>Note for jalview applet users: due to the applet security
-constraints, PDB Files can currently only be imported by cut and paste
-of the PDB file text into the text box opened by the 'From File' entry
-of the structure menu.</p>
+ href="seqfetch.html">Sequence Fetcher</a>. Any sequences retrieved with
+this service are automatically associated with their source database
+entry. For PDB sequences, simply select PDB as the database and enter
+your known PDB id (appended with ':' and a chain code, if desired).<br>
+Jalview will also read PDB files directly. Simply load in the file as
+you would an alignment file. The sequences of any peptide chains will be
+extracted from the file and viewed in the alignment window.</p>
+
+<p><em>Note for jalview applet users:<br>
+Due to the applet security constraints, PDB Files can currently only be
+imported by cut and paste of the PDB file text into the text box opened
+by the 'From File' entry of the structure menu.</em></p>
+
<p><strong>Viewing the PDB Residue Numbering</strong><br>
Sequences which have PDB entry or PDB file associations are annotated
with sequence features from a group named with the associated PDB
-accession number or file name. Each feature gives the corresponding
-PDB Residue Number for each mapped residue in the seuqence. The
-display of these features is controlled through the
-<strong>"View→Sequence Features"</strong> menu item
-and the <a href="featuresettings.html">Feature Settings dialog
-box</a>.</p>
+accession number or file name. Each feature gives the corresponding PDB
+Residue Number for each mapped residue in the sequence. The display of
+these features is controlled through the <strong>"View→Sequence
+Features"</strong> menu item and the <a href="featuresettings.html">Feature
+Settings dialog box</a>.</p>
+
+<p><em><strong>Outstanding problem with cut'n'pasted
+files in Jalview 2.6</strong><br>
+Structures imported via the cut'n'paste dialog box will not be correctly
+highlighted or coloured when they are displayed in structure views,
+especially if they contain more than one PDB structure. See the bug
+report at http://issues.jalview.org/JAL-623 for news on this problem.</em></p>
</body>
</html>
+
git://source.jalview.org / jalview.git / commitdiff