From dbb8e925003ee2249a65bed6e6c74b378b673a18 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Fri, 17 Apr 2015 10:19:52 +0100 Subject: [PATCH] JAL-1668 updated documentation --- help/html/features/chimera.html | 10 +- help/html/features/jmol.html | 4 +- help/html/features/viewingpdbs.html | 53 ++++-- help/html/menus/popupMenu.html | 337 ++++++++++++++++++----------------- 4 files changed, 218 insertions(+), 186 deletions(-) diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html index 31ca419..11b43c8 100644 --- a/help/html/features/chimera.html +++ b/help/html/features/chimera.html @@ -32,7 +32,7 @@ id pop-up menu (if you can't see this, then you need to

You can set a default choice of Jmol or Chimera structure viewer in Preferences. You can also optionally specify the path to the Chimera program here (if it differs from the standard paths searched by Jalview). -

The following menu entries are provided for viewing structure data
+

Superposing structures based on their aligned sequences
-

If several structures are available on the alignment, you may add +If several structures are available on the alignment, you may add additional structures to an existing Chimera 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 @@ -63,12 +63,12 @@ menu bar of the structure view window to superpose the structures using the updated alignment.

Chimera Controls
-

The structure is by default rendered as a ribbon diagram. Moving the +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 ([RES]Num:Chain). Moving the mouse over an associated residue in an alignment window highlights the associated -atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.

+atoms in the displayed structures. For comprehensive details of Chimera's commands, refer to the tool's Help menu.

Basic screen operations (see Chimera help (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html) for full details). diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index ce1b834..c81fcc3 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -33,7 +33,7 @@ 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.

-

The following menu entries are provided for viewing structure data
+

Superposing structures based on their aligned sequences
If several structures are available on the alignment, you may add diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index c342bc9..bece211 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -23,12 +23,30 @@ PDB Viewing -

Viewing PDB Structures

- Jalview can view protein structures associated with a sequence via the - "Structure→" submenu from a sequence's pop-up menu. + Viewing PDB Structures

+ Jalview can be used to view protein structures by following the steps below: +
    +
  1. Select the "View Structure" option from a + sequence's pop-up menu. +
      +
    • If one or more structures exists for the given sequence, the 'Structure Chooser' + dialogue is opened with a list of the found structures meta-data.
      • +
    • However, if no structure was found, the 'Structure Chooser' dialogue is opened with options for manual association of PDB structures.
      • +
    +
    2. +
  2. 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.
    3. +
  3. When the desired structure(s) have been selected, they can be + viewed by clicking the "View" button below the summary list. +
    4. + +
+ The Jmol viewer has been included since Jalview 2.3. Jalview 2.8.2 included support for Chimera, provided it is @@ -42,7 +60,8 @@ href="xsspannotation.html">Annotation from Structure page for more information.

-

The following menu entries are provided for viewing structure data
+ -

If a single pdb +

If a single pdb structure is selected, one of the following will happen:

Associating PDB files with Sequences

-

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:

+

Since Jalview 2.8.3, discovery of PDB Id associated to a sequence happens automatically when the "View Structure" option is selected + from a sequence's pop-up menu. Jalview uses the sequence's ID to query the PDB Rest API, provided by the + EBI to discover PDB ids associated with the sequence.

+ +

Manual association of PDB files with Sequences

+

To manually associate PDB files with a sequence, right click on a sequence +ID and select the "View Structure" option, this opens the 'Structure Chooser' dialogue. Then pick any of the follwing options listed below from the drop-down menu in the 'Structure Chooser' panel to proceed with manual association:

+Note: 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. +

Importing PDB Entries or files in PDB format
You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 6bb2e3a..f84922e 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -24,138 +24,158 @@ -

Popup Menu
-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).

-