X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=6c10e98fa90c9c9907ba3c560a68a77e4db18ca4;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=a6f5de92aeb857e8cb762db906da14ad7f2b2f55;hpb=46e848e62edcdfd0a135d313128456bb69055009;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index a6f5de9..6c10e98 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,20 +1,21 @@ PDB Viewing @@ -38,14 +39,24 @@ structure is selected, one of the following will happen:

  • If the structure is already shown, then you will be prompted to associate the sequence with an existing view of the selected - structure.
    • + structure. This is useful when working with multi-domain or multi-chain PDB files.
  • See the Jmol PDB viewer help page for more information about the display.
    • - - -

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

    + 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 Sequence", and one of the submenus:

    @@ -60,9 +71,8 @@ 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