PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=c342bc9d52e8177101c4782edc736f8ccf4a1d69;hb=f27f81a74bbe1be141d23df8aba578515e3179a2;hp=679f35303af73c34f709b32761589352d37c64b0;hpb=793968f15efc19ba0b8a91b0078e6b23ee4e2ff9;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 679f353..c342bc9 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,59 +1,88 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> 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. +

+ The + Jmol viewer has been included since Jalview + 2.3. Jalview 2.8.2 included support for Chimera, provided it is + installed and can be launched by Jalview. The default viewer can be + configured in the + Structure tab in the + Tools→Preferences dialog box. +

+ Structure data imported into Jalview can also be processed to display + secondary structure and temperature factor annotation. See the Annotation from Structure page for + more information. +

The following menu entries are provided for viewing structure data
+

The "Structure→View + Structure→ submenu allows a single PDB structure to be chosen + for display from the available structures for a sequence. +
The "Structure→View all N + structures + option will open a new window containing all structures associated + with the current selection, superposed according to the currently selected region of the alignment.
This + capability was added in Jalview 2.7 +
The "Structure→View all N + representative structures + option will open a new window containing exactly one structure per + currently selected sequence.
+ The View representative structures option was introduced in + Jalview 2.8.1

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 +

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

If no structures are open, then an interactive display of the - structure will be opened in a new window
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)

new feature in Jalview 2.6

If the structure is already shown, then you will be prompted to associate the sequence with an existing view of the selected - structure.
See the Jmol - PDB viewer help page for more information about the display.

Chimera

- -

- Additionally, if several of the sequences in the currently selected - region of the alignment have associated structures, then Jalview will - provide a 'View X structures' entry in the submenu. This - option will open a new Jmol view containing 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:

@@ -69,9 +98,8 @@ 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