PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=44a07cc5847c567be8bf7a821c61d05584e63a6d;hb=023d23abaad346f745b93fced2407d7342ab7171;hp=c342bc9d52e8177101c4782edc736f8ccf4a1d69;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index c342bc9..44a07cc 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -23,12 +23,29 @@ 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. + Viewing PDB Structures

+ Jalview can be used to view protein structures by following the steps below: +

Select the "View Structure" option from a + sequence's pop-up menu to invoke the Structure Chooser interface. +
- If one or more structures exists for the given sequence, the Structure Chooser + dialogue is opened with a list of the found structures meta-data.
- However, if no structure was found, the Structure Chooser interface is opened with options for manual association of PDB structures.
+
Choose the structure to view from the discovered list. This can be done either manually by clicking directly + on the desired structure(s) in the list, or automatically by + using the drop-down menu on the interface to filter and auto-select the best structure based on certain + criteria like quality, resolution, etc.
When the desired structure(s) have been selected, they can be + viewed by clicking the "View" button below the summary list. +

+ The Jmol viewer has been included since Jalview 2.3. Jalview 2.8.2 included support for Chimera, provided it is @@ -42,7 +59,8 @@ href="xsspannotation.html">Annotation from Structure page for more information.

The following menu entries are provided for viewing structure data
+ -

If a single pdb +

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

See the Jmol and Chimera PDB viewer help pages for more information about the display.

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:

From File - You can load a PDB file from the local machine or - network and associate it with the selected sequence. PDB files - associated in this way will also be saved in the Jalview Archive file.
-
Enter PDB Id - Jalview will use WSDBFetch, provided by the - EBI, to fetch the PDB file with the entered Id.
-
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
You can retrieve sequences from the PDB using the 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.