From: Jim Procter Date: Mon, 5 Sep 2016 16:16:43 +0000 (+0100) Subject: JAL-2089 reworked and formatted doc for X-Git-Tag: Release_2_10_0~47^2~5^2~2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ac4f3dfaa8d22b7b2eb164cceb354d029c07b0ad;p=jalview.git JAL-2089 reworked and formatted doc for JAL-1666 PDB search interface and ‘3D structure…’ viewing option JAL-1919 mmcif --- diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index d4819f1..e62b2a7 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -24,10 +24,10 @@

- Viewing PDB Structures + Discovering and Viewing PDB Structures

- Jalview can be used to view protein structures by following the steps - below: + Jalview can be used to explore the 3D structures of sequences in an + alignment by following the steps below:

Select the "3D Structure Data..." option from a sequence's pop-up @@ -40,18 +40,18 @@ pane.

However, if no structure was found, the Structure Chooser interface will present options for manual - association of PDB structures. + href="structurechooser.html">Structure Chooser interface + will present options for manual association of PDB structures.
Selecting Structures
If structures - have been discovered, then some will already be selected according - to predefined selection criteria, such as structures with the - highest resolution. Use the drop down menu to select structures - according to different criteria, or, alternatively, choose - structures manually by selecting with the keyboard and mouse. +
Selecting Structures
You can select + the structures to you want to open and view by selecting them with + the mouse and keyboard.
By default, if structures were + discovered, then some will already be selected according to the + criteria shown in the drop-down menu. The default criteria is + 'highest resolution', simply choose another to pick structures in + a different way.
- Viewing Cached Structures
  If you have previously downloaded structures for your sequences, they @@ -89,9 +89,8 @@
- 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). + href="jmol.html#align">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 @@ -107,31 +106,20 @@
  - 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 protein or - nucleotide chains will be extracted from the file and viewed in the - alignment window. + Retrieving sequences from the PDB
  You can + retrieve sequences from the PDB using the Sequence Fetcher. The sequences + retrieved with this service are derived directly from the PDB 3D + structure data, which can be viewed in the same way above. Secondary + structure and temperature factor annotation can also be added.
  
  -
  - Importing PDB Entries or files in mmCIF format
  - mmCIF file format provides an alternative means for - importing 3D structure data from flat file and EMBL-PDBe - web-service. To enable mmCIF as the default format for - importing PBD sequences from the PDB sequence fetcher, add or modify the - property - DEFAULT_STRUCTURE_FORMAT=mmCIF in Jalview properties file. - Once this is done, the steps followed in retrieving PDB format files above can - be followed to obtain the same data with mmCIF. mmCIF format file support was added in Jalview 2.9.1.
  - - + Retrieving sequences from the PDB
  Jalview + will also read PDB files directly - either in PDB format, or mmCIF. Simply load in the file as you would + an alignment file. The sequences of any protein or nucleotide chains + will be extracted from the file and viewed in the alignment window. +
  
  Associating a large number of PDB files to @@ -142,8 +130,8 @@ desktop, Jalview will give you the option of associating PDB files with sequences that have the same filename. This means, for example, you can automatically associate PDB files with names like '1gaq.pdb' - with sequences that have an ID like '1gaq'.
  - Note: This feature was added in Jalview 2.7 + with sequences that have an ID like '1gaq'.
  Note: + This feature was added in Jalview 2.7
  
  Note for Jalview applet users:
  Due to the applet @@ -163,16 +151,31 @@ Features" menu item and the Feature Settings dialog box.
  +
  +
  +
  + Switching between mmCIF and PDB format for + downloading files from the PDB
  Jalview now employs the mmCIF format for importing 3D structure data + from flat file and EMBL-PDBe web-service, as recommended by the + wwwPDB. If you prefer (for any reason) to download data as PDB files + instead, then first close Jalview, and add the following line to + your .jalview_properties file:
  + DEFAULT_STRUCTURE_FORMAT=PDB +
  When this setting is configured, Jalview will only request + PDB format files from EMBL-EBI's PDBe.
  mmCIF format + file support was added in Jalview 2.10. +
  
  Outstanding problem with cut'n'pasted - files in Jalview 2.6 and Jalview 2.7
  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/browse/JAL-623 for - news on this problem. + files in Jalview 2.6 and Jalview 2.7
  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/browse/JAL-623 for news on this problem.
  +