X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=412a23ae0283b8165f9a1d150835c958db7c3b74;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=71c201154d44a1905fa88068e0089e22de2dc991;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 71c2011..412a23a 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,20 +1,21 @@ PDB Viewing @@ -23,8 +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:

 - - -

To associate PDB files with a sequence, right click on a sequence +

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:

@@ -60,9 +83,8 @@ Sequence", and one of the submenus:

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.
    • +
  • Discover PDB Ids - Jalview uses the sequence's ID to query WSDBFetch, provided by the + EBI, and any enabled DAS servers, to discover PDB ids associated with the sequence.

    • Importing PDB Entries or files in PDB format
    @@ -75,6 +97,18 @@ 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.

    +

    +Associating a large number of PDB files to sequences +in an alignment
    It is often the case when working with +structure alignments that you will have a directory of PDB files, and +an alignment involving one or more of the structures. If you drag a +number of PDB files onto an alignment in the Jalview 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 +

    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 @@ -90,11 +124,11 @@ Features" menu item and the Feature Settings dialog box.

    Outstanding problem with cut'n'pasted -files in Jalview 2.6
    +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/JAL-623 for news on this problem.

    +report at http://issues.jalview.org/browse/JAL-623 for news on this problem.