PDB Viewing

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=f9932044ba807aaea55ce49057ed97698aaa5769;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d979254bc39181c5f97284ec772306b4b2a3e6a1;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index d979254..f993204 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,68 +1,165 @@ -PDB Viewing + * 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→View - PDB entry:" entries from a sequence's pop-up menu. This will open an - interactive display of the structure in a new window, or prompt you - 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. -

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.
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Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch - the PDB file with the entered Id.
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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.

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.

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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 seuqence. The -display of these features is controlled through the -"View→Sequence Features" menu item -and the Feature Settings dialog -box.
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+ Viewing PDB Structures +
+ Jalview can be used to view protein structures by following the steps + below: +
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Select the "3D Structure Data..." option + from a sequence's pop-up + menu to open the Structure + Chooser dialog box. +
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If one or more structures exists for the given + sequence, the Structure + Chooser dialog will open with them listed in the results + pane. +
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However, if no structure was found, the Structure Chooser interface will present options for manual + association of PDB structures. +
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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. +
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Viewing Cached Structures
If you + have previously downloaded structures for your sequences, they + can be viewed by selecting the Cached PDB + Entries option from the drop down menu at the top of the + dialog box.
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To view selected structures, click the "View" + button. +
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+ + 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. +
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+ If a single PDB structure is selected, one of the + following will happen: +
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If no structures are open, then an interactive display of + the structure will be opened in a new window.
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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). +
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If the structure is already shown, then you will be + prompted to associate the sequence with an existing view of the + selected structure. This is useful when working with multi-domain + or multi-chain PDB files.
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See the Jmol + and Chimera PDB viewer help pages for + more information about the display. +
+
+ + +
+ 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 protein or + nucleotide chains will be extracted from the file and viewed in the + alignment window. +
+ +
+ Associating a large number of PDB files to + sequences in an alignment
It is often the case when working + with structure alignments that you will have a directory of PDB + files, and an alignment involving one or more of the structures. If + you drag a number of PDB files onto an alignment in the Jalview + desktop, Jalview will give you the option of associating PDB files + with sequences that have the same filename. This means, for example, + you can automatically 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:
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. +
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+ Outstanding problem with cut'n'pasted + files in Jalview 2.6 and Jalview 2.7
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/browse/JAL-623 for + news on this problem. +
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