X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=71c201154d44a1905fa88068e0089e22de2dc991;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=353ca09aac7d5ad2473333b4e23c43edb5817740;hpb=83b541e967d19e6aeb5b02f476a77399f5f79d22;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 353ca09..71c2011 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,41 +1,100 @@ - -
Viewing PDB Structures
-Jalview has a simple 3D structure viewer which - can visualize polypeptide backbone structures associated with a sequence in - a particular alignment view. It is accessed via the "Sequence→View - PDB entry:" entry from the sequence's pop-up menu.
-Since Jalview 2.3, Jmol has been integrated into the application and will also - run in the applet in all latest web browsers. For more help using Jmol, see - http://jmol.sourceforge.net/docs/JmolUserGuide/ -
-To associate PDB files with a sequence, right click on a sequence ID and select - "Associate Structure with Sequence", and one of the submenus:
-Note: You can retrieve sequences from the PDB using the 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).
-Sequences which have PDB File associations are annotated with sequence features - from the group 'PDBFile' giving the corresponding PDB Residue Number for each - mapped residue in the seuqence. The display of these features is controlled through - the "View→Sequence Features" menu item and the - Feature Settings dialog box.
-See the PDB Viewer help page for more information.
- - + + + +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 +structure is selected, one of the following will happen:
+ +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:
+ +Importing PDB Entries or files in PDB format
+You can retrieve sequences from the PDB using the 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
+extracted from the file and viewed in the alignment window.
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.
Viewing the PDB Residue Numbering
+Sequences which have PDB entry or PDB file associations are annotated
+with sequence features from a group named with the associated PDB
+accession number or file name. Each feature gives the corresponding PDB
+Residue Number for each mapped residue in the sequence. The display of
+these features is controlled through the "View→Sequence
+Features" menu item and the Feature
+Settings dialog box.
Outstanding problem with cut'n'pasted
+files in Jalview 2.6
+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.