From: tcofoegbu Date: Wed, 22 Apr 2015 15:47:55 +0000 (+0100) Subject: Merge branch 'features/JAL-1667_1668-documentation' into Release_2_8_3_Branch X-Git-Tag: Jalview_2_9~56^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=830a19575c85366f00f6025f9fe98ef8298fc289;hp=f27f81a74bbe1be141d23df8aba578515e3179a2;p=jalview.git Merge branch 'features/JAL-1667_1668-documentation' into Release_2_8_3_Branch --- 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/pdbseqfetcher.png b/help/html/features/pdbseqfetcher.png new file mode 100644 index 0000000..b243168 Binary files /dev/null and b/help/html/features/pdbseqfetcher.png differ diff --git a/help/html/features/pdbsequencefetcher.html b/help/html/features/pdbsequencefetcher.html new file mode 100644 index 0000000..0412a5f --- /dev/null +++ b/help/html/features/pdbsequencefetcher.html @@ -0,0 +1,83 @@ + + + +PDB Sequence Fetcher + + + + PDB Sequence Fetcher +

From Jalview 2.x.x a speciliased interface was introduced for + fast and efficient discovery/retrieval of sequence data from the PDB + database. The introduced interface enables live querying of PDB data + on-the-fly thereby eliminating the need to memorise database accession + or to cross-reference other bioinformatics websites before retrieving + a sequence data in jalview. The underlying technology is provided by + EBI and is based on Apache Solr which is a text based search engine.

+ +

+ The PDB Sequence Fetcher interface can be opened by selecting PDB + as the choice database from the 'Select Database + Retrieval Source' interface of Sequence + Fetcher. +

+ + PDB sequence fetcher (introduced in Jalview 2.x.x) + + +

+ Searching the PDB Database
Once the + interface is opened, typing in the search text box will execute a live + query to the PDB database and display the results on-the-fly as seen + in the screen-shot above. Use the drop-down menu to select a specific + field to search by in the PDB database, the default option is 'ALL'. +
+ +
Wild card searching: The PDB sequence fetcher also provides support for wild card querying of the PDB database. +
Single character (matches a single character) - ? + The search string te?t would match both test and text. + +
Multiple characters (matches zero or more sequential characters) - * + +The wildcard search: +tes* - would match test, testing, and tester. + + +You can also use wildcard characters in the middle of a term. For +example: +te*t - would match test and text. +*est - would match pest and test. +

+ +

+ Customising displayed meta-data
To change the + displayed meta-data in the search result, click the 'Configure + Displayed Columns' tab, then tick off the options wanted. +

+

Importing Sequence
+ After querying the PDB database, to import the found data into Jalview, select the entries you wish to import then click the ok button at the bottom of the interface.

+

+ The PDB Sequence Fetcher interface was introduced in Jalview + 2.x.x. +

+ + \ No newline at end of file diff --git a/help/html/features/schooser_enter-id.png b/help/html/features/schooser_enter-id.png new file mode 100644 index 0000000..dc5aa93 Binary files /dev/null and b/help/html/features/schooser_enter-id.png differ diff --git a/help/html/features/schooser_main.png b/help/html/features/schooser_main.png new file mode 100644 index 0000000..fe9e5dc Binary files /dev/null and b/help/html/features/schooser_main.png differ diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index fa61e1a..68c5520 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -49,6 +49,7 @@ WSDBFetch service provided by the European Bioinformatics Institute, or, since J one or more accession ids (as a semi-colon separated list), or press the "Example" button to paste the example accession for the currently selected database into the retrieval box. Finally, press "OK" to initiate the retrieval.

+

Since Jalview 2.x.x if PDB is selected as the sequence database, a specialised interface - PDB Sequence Fetcher is used for discovering and retrieving the sequenec data.

Specifying chains for PDB IDs If you are retrieving sequences from the PDB, you can retrieve specific chains by appending a colon and the chain id to the PDB diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html new file mode 100644 index 0000000..7dd69c1 --- /dev/null +++ b/help/html/features/structurechooser.html @@ -0,0 +1,109 @@ + + + +Structure Chooser + + + +

+ Structure Chooser +

+ + The Structure Chooser interface provides a smart technique for + selecting PDB structures to view in Jalview by querying readily + available meta-data of structures. The Interface can be invoked by selecting + the + "View Structure" option from a sequence's + pop-up menu. Some of the main + features it provides are listed below: + + Additionally, the Structure Chooser retains the following contemporary + features of Jalview: + + + + Associating PDB files with Sequences
+ Discovery/Association of PDB entries to a sequence happens + automatically during the initialisation of the Structure Chooser + Interface. Jalview uses the sequence's ID to query the PDB Rest API, + provided by the EBI to discover PDB Ids associated with the sequence. + +

+ Configuring displayed meta-data for Structures
+ To configure the visible meta-data displayed for the discovered structures, click the 'Configure Displayed Columns' tab, then tick the options which you intend to make visible. + +

+ Auto-selection of best Structures +
Jalview can automatically filter and select the best structures using various metric categories avaialble from the meta-data + of the structures. To perform this simply select any of the following options from the drop-down menu in the Structure + Chooser interface: Best Uniprot coverage, Higest Resolution, + + Best Quality, Highest Protein Chain etc. When the 'Invert' option is selected, Jalview returns an inverse result for the current selected option in the drop-down menu.

+ + +
The screenshot above shows the Structure Chooser interface + along with the meta-data of auto-discovered structures for the sample + alignment. Note however that if no structures were auto-discovered, a + different interface for manual association will be invoked as seen in + the screenshot below. +

+ +

+ Manual selection/association of PDB files with Sequences +

+

To manually associate PDB files with a sequence, select any of + the follwing options listed below from the drop-down menu in the + interface: +

+ +

+ The Structure Chooser interface was introduced in Jalview 2.x.x. + +

+ + \ No newline at end of file diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index c342bc9..506beef 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -23,12 +23,29 @@ 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 to invoke the Structure Chooser interface. +
      +
    • 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 interface is opened with options for manual association of PDB structures.
      • +
    +
    2. +
  2. Choose the structure to view from the discovered list. This can be done either manually by clicking directly + on the desired structure(s) in the list, or automatically by + using the drop-down menu on the interface to filter and auto-select the best structure based on certain + criteria like quality, resolution, etc.
    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 +59,8 @@ 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:

-

Importing PDB Entries or files in PDB format
You can retrieve sequences from the PDB using the -

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).

-