From 8d0464e6227795ef73b337205ce7f586976bb70c Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sat, 17 May 2014 12:55:19 +0100 Subject: [PATCH] JAL-1477 documentation and tooltips --- help/html/features/jmol.html | 23 +++++++++++++++++++-- help/html/features/pdbviewer.html | 8 +++++--- help/html/features/viewingpdbs.html | 38 +++++++++++++++++++++++------------ help/html/menus/popupMenu.html | 22 ++++++++++++++++++-- resources/lang/Messages.properties | 6 +++--- 5 files changed, 74 insertions(+), 23 deletions(-) diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html index b3c3570..19f1761 100644 --- a/help/html/features/jmol.html +++ b/help/html/features/jmol.html @@ -24,14 +24,33 @@

The Jmol PDB Viewer

Since Jalview 2.3, Jmol has been integrated into Jalview for interactively viewing structures -opened by selecting the "Structure→View PDB -entry:" option in the sequence +opened by entries in the "Structure" submenu 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.

+

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/pdbviewer.html b/help/html/features/pdbviewer.html index 10924a5..c1c6ae7 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -29,9 +29,11 @@ PDB viewer, which is only used in situations where Jmol is unavailable or cannot operate.

The PDB Viewer Window

This 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 +entries from the "Structure→" submenu + of the sequence + id pop-up menu. The internal PDB viewer is not able to show + superpositions, so no other options are provided. Structures can only + be viewed for sequences which have an associated PDB structure, and the PDB Viewer will only be associated with the particular alignment view from which it was opened.

Controls

diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 6c10e98..144489b 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -24,8 +24,31 @@

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. Once a pdb +via the "Structure→" submenu from a +sequence's pop-up menu.

+

The following menu entries are provided for viewing structure data
+

+
+

+ +

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

-

- Opening structures associated with the current selection
- If one or more of the sequences in the alignment are selected, then - the Structure submenu of the Sequence - ID popup menu will contain will include either a 'View all X - structures' entry in the submenu or a 'View structure for Sequence' - entry. Both these options will open a new Jmol view containing one, or - all the structures available for all selected sequences, superimposed - using the currently selected region of the alignment. (This - capability was added in Jalview 2.7) -

Associating PDB files with Sequences

To associate PDB files with a sequence, right click on a sequence ID and select "Structure→ Associate Structure with diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 6ceccee..71b2603 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -148,11 +148,11 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

  • From File
    Load a PDB file from local disk which will be associated with this sequence. This file will be used if the user subsequently - clicks on "View PDB Structure" menu item.
    • + clicks on "View Structure" menu item.
  • Enter PDB id
    Enter the PDB id from an input window. This PDB id will be used by the service WSDBFetch, provided by the EBI, to fetch the - PDB file if the user subsequently clicks on "View PDB Structure" + PDB file if the user subsequently clicks on its "View Structure" menu item.
  • Discover PDB ids
    This will use the service WSDBFetch, provided by the @@ -169,6 +169,24 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

    href="../features/viewingpdbs.html">associated PDB structures.
    If the sequence or alignment has RNA structure, then 2D RNA entries will also be present enabling you to open a linked view of the RNA structure in VARNA.
    • +

    Other menu entries may also be shown if the current selection includes sequences with associated structure data:
    +

    +
  • + +
  • Hide Sequences
    diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 906db68..6736791 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -463,8 +463,8 @@ label.jalview_cut = Cut (Jalview Only) label.to_upper_case = To Upper Case label.to_lower_case = To Lower Case label.toggle_case = Toggle Case -label.edit_name_description = Edit Name/Description -label.create_sequence_feature = Create Sequence Feature +label.edit_name_description = Edit Name/Description ... +label.create_sequence_feature = Create Sequence Feature ... label.edit_sequence = Edit Sequence label.edit_sequences = Edit Sequences label.sequence_details = Sequence Details @@ -629,7 +629,7 @@ label.edit_name_and_description_current_group = Edit name and description of cur label.view_structure_for = View structure for {0} label.view_all_structures = View all {0} structures. label.view_all_representative_structures = View all {0} representative structures. -label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = "Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment." +label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment = Opens a new Jmol view with all representative structures\nassociated with the current selection\nsuperimposed with the current alignment. label.associate_structure_with_sequence = Associate Structure with Sequence label.from_file = from file label.enter_pdb_id = Enter PDB Id -- 1.7.10.2