X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=6419525bb243963645a87cde9cf28d36ab2909fc;hb=141040cac1e8570634a25ad6a5550a56558041fb;hp=bece211d0a597f726b54cae24ae319d7412aebb0;hpb=dbb8e925003ee2249a65bed6e6c74b378b673a18;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index bece211..6419525 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -28,24 +28,31 @@

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. +
  2. Select the "3D Structure Data..." option from a + sequence's pop-up menu to open the Structure Chooser dialog box.
    3. -
  3. 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.
    4. -
  4. When the desired structure(s) have been selected, they can be - viewed by clicking the "View" button below the summary list. -
    5. - -
+
  • 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. +
    • +
  • To view selected structures, click the "View" + button. +
    • + The Jmol viewer has been included since Jalview @@ -60,29 +67,8 @@ href="xsspannotation.html">Annotation from Structure page for more information.

    - -

    If a single pdb +

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

    -

    Associating PDB files with Sequences

    -

    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 + href="pdbsequencefetcher.html">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 peptide chains will be +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.

    @@ -145,7 +111,7 @@ 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:
    +

    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 by the 'From File' entry of the structure menu.