From fd0e6b1ca56431d0aa68f64d8f5ff33bfee5b0ec Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 22 Sep 2010 10:43:01 +0000 Subject: [PATCH] Jmol 12 update --- help/html/features/jmol.html | 142 ++++++++++++++++++++++------------- help/html/features/viewingpdbs.html | 110 +++++++++++++++++---------- 2 files changed, 162 insertions(+), 90 deletions(-) diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index e7f963b..3233192 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -15,31 +15,43 @@ * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . ---> +--> The Jmol PDB Viewer -

The Jmol PDB Viewer -

The interactive structure viewing window is opened by selecting -the "Sequence→View PDB entry:" entry in -the sequence id pop-up menu. This -can only be done for sequences which have an associated -PDB structure. +

The Jmol PDB Viewer

Since Jalview 2.3, Jmol -has been integrated into Jalview. It is automatically used by the -application, and should also run in the applet in all latest web -browsers. If jmol is not available, then the original internal pdb viewer will be used as a fallback. +has been integrated into Jalview for interactively viewing structures +opened by selecting the "Sequence→View PDB +entry:" option in the sequence +id pop-up menu (if you can't see this, then you need to associate a PDB structure with the +sequence). Jmol is available from the Jalview desktop and should also +run in the JalviewLite applet, providing the browser supports Java 1.5. +If Jmol is not available, then the original internal +pdb viewer will be used as a fallback.

+

Superposing structures based +on their aligned sequences
+If several structures are available on the alignment, you may add +additional structures to an existing Jmol view by selecting their entry +in the appropriate pop-up menu. Jalview will ask you if you wish to add +the structure to the existing alignment, and if you do, it will import +and superimpose the new PDB file using the corresponding positions from +the alignment. If the alignment is subsequently edited, you can use the +Jmol→Align menu option from the +menu bar of the structure view window to superpose the structures using +the updated alignment.
+Sequence based structure superposition was added in Jalview 2.6

-

Controls

-

The structure is by default rendered as a ribbon diagram. Moving the -mouse over the structure brings up tooltips giving the residue name, -PDB residue number and chain code, atom name and number +

Controls
+The structure is by default rendered as a ribbon diagram. Moving the +mouse over the structure brings up tooltips giving the residue name, PDB +residue number and chain code, atom name and number ([RES]Num:Chain.AtomName#AtomNumber). If a mapping exists to a residue -in any associated sequences, then this will be highlighted in each -one's alignment window. The converse also occurs - moving the mouse -over an associated residue in an alignment window highlights the associated +in any associated sequences, then this will be highlighted in each one's +alignment window. The converse also occurs - moving the mouse over an +associated residue in an alignment window highlights the associated atoms in the displayed structures.

Selecting a residue highlights its associated sequence residue and alpha carbon location. Double clicking an atom allows distances to @@ -60,9 +72,11 @@ be measured from it to any other atom in the structure.

Zoom - Shift + Left Click
drag mouse up or down - Shift + Left Click
or middle button
drag - mouse up or down + Shift + Left Click
+ drag mouse up or down + Shift + Left Click
+ or middle button
+ drag mouse up or down Left-Alt + Click and drag mouse up or down @@ -75,17 +89,23 @@ be measured from it to any other atom in the structure.

Roll View - Shift + Left Click
drag mouse to left or - right - Shift + Left Click
or middle button
drag mouse to left or right + Shift + Left Click
+ drag mouse to left or right + Shift + Left Click
+ or middle button
+ drag mouse to left or right Left-Alt + Click and drag mouse to left or right Move Origin - Shift+Control+Left Click
or Middle Button
+ Shift+Control+Left Click
+ or Middle Button
+ Drag - Middle-Button
and
drag - Shift+Control+Left Click
or Middle Button
+ Middle-Button
+ and
+ drag + Shift+Control+Left Click
+ or Middle Button
and drag @@ -96,13 +116,14 @@ be measured from it to any other atom in the structure.

-

The window has four menus: +

The window has up to five menus:

-

Functionality provided by Jmol -

The Jmol menu provides access to a number of features for +

Functionality provided by Jmol

+

Jmol's own functions are accessed by clicking the 'Jmol' logo or +right-clicking in the structure display area. Either way will open the +Jmol pop-up menu, which provides access to a number of features for controlling the colour and display of molecules, adding measurements and -labels, plotting surfaces, and display animation. The 'Set Picking' -menu controls the behaviour of single and double mouse clicking on the -structure.

+labels, plotting surfaces, and display animation. The 'Set Picking' menu +controls the behaviour of single and double mouse clicking on the +structure, and the 'Console' option opens the Jmol scripting console.

The state of each Jmol display is stored within jalview archives as a jmol state recovery script -file. This means that any Jmol visualization effects that -you add beyond those provided by Jalview will be able to be stored and -recovered along with the displayed alignments in Jalview. -

More Information -

Jmol is a sophisticated program in its own right, with its own + href="jalarchive.html">jalview archives as a Jmol state recovery +script file. This means that any Jmol visualization effects that you add +beyond those provided by Jalview will be able to be stored and recovered +along with the displayed alignments in Jalview.

+

More Information

+

Jmol is a sophisticated program in its own right, with its own command console and scripting language. Only the essentials have been -described here - the interested reader is referred to -Jmol's own comprehensive -online documenation.

+described here - the interested reader is referred to Jmol's own comprehensive +online documentation.

+

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index d979254..cf6671e 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -16,53 +16,85 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> -PDB Viewing + +PDB Viewing +

Viewing PDB Structures

-

Jalview can view protein structures associated with a sequence via the "Structure→View - PDB entry:" entries from a sequence's pop-up menu. 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 Jmol PDB viewer help page - for more information about the display. -

-

To associate PDB files with a sequence, right click on a sequence ID and select - "Structure→ Associate Structure with Sequence", - and one of the submenus:

+ +

Jalview can view protein structures associated with a sequence +via the "Structure→View PDB entry:" entries from a +sequence's pop-up menu. Once a pdb +structure is selected, one of the following will happen:

+
    -
  • 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 Jalview Archive file.
    -
    • -
  • Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch - the PDB file with the entered Id.
    -
    • -
  • 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.
    • +
  • If no structures are open, then an interactive display of the + structure will be opened in a new window
    • + +
  • If another structure is already shown for the current + alignment, then you will be asked if you want to add and align this structure to the structure in + the existing view. (new feature in Jalview 2.6)
    • + +
  • If the structure is already shown, then you will be prompted + to associate the sequence with an existing view of the selected + structure.
    • + +
  • See the Jmol + PDB viewer help page for more information about the display.
+ + +

To associate PDB files with a sequence, right click on a sequence +ID and select "Structure→ Associate Structure with +Sequence", and one of the submenus:

+ +
    +
  • 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 Jalview Archive file.
    +
    • + +
  • Enter PDB Id - Jalview will use WSDBFetch, provided by the + EBI, to fetch the PDB file with the entered Id.
    +
    • + +
  • 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.
    • +
+

Importing PDB Entries or files in PDB format
You can retrieve sequences from the PDB using the Sequence Fetcher. 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). -
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. -
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.

+ href="seqfetch.html">Sequence Fetcher. 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).
+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.

+ +

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.

+

Viewing the PDB Residue Numbering
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 -"View→Sequence Features" menu item -and the Feature Settings dialog -box.

+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 "View→Sequence +Features" menu item and the Feature +Settings dialog box.

+ +

Outstanding problem with cut'n'pasted +files in Jalview 2.6
+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.

+ -- 1.7.10.2