X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;fp=help%2Fhtml%2Ffeatures%2Fviewingpdbs.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=b1ad4bae86c77cc534a3285c370a2a3e864cb54e;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html deleted file mode 100755 index b1ad4ba..0000000 --- a/help/html/features/viewingpdbs.html +++ /dev/null @@ -1,190 +0,0 @@ - - - -PDB Viewing - - -

- Discovering and Viewing PDB Structures -

- Jalview can be used to explore the 3D structures of sequences in an - alignment by following the steps below: -
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  1. Select the "3D Structure Data..." option - from a sequence's pop-up - menu to open the Structure - Chooser dialog box. - -
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  2. Selecting Structures
    You can select - the structures that you want to open and view by selecting them - with the mouse and keyboard.
    By default, if structures were - discovered, then some will already be selected according to the - criteria shown in the drop-down menu. The default criteria is - 'highest resolution', simply choose another to pick structures in - a different way.
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  3. To view selected structures, click the "View" - button. -
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- Structure Viewers in the Jalview Desktop
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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Controlling where the new structures - will be shown -
The Structure Chooser offers several options - for viewing a structure.
New View will open a new - structure viewer for the selected structures, but if there are views - already open, you can select which one to use, and press the Add - button. Jalview can automatically superimpose new structures based - on the linked alignments - but if this is not desirable, simple - un-tick the Superpose Structures checkbox. - -

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- Superposing structures
Jalview superposes structures using - the visible portions of any associated sequence alignments. A - message in the structure viewer's status bar will be shown if not - enough aligned columns were available to perform a superposition. -

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- See the Jmol - and Chimera help pages for - more information about their capabilities.

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- Retrieving sequences from the PDB
You can - retrieve sequences from the PDB using the Sequence Fetcher. The sequences - retrieved with this service are derived directly from the PDB 3D - structure data, which can be viewed in the same way above. Secondary - structure and temperature factor annotation can also be added.
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Jalview will also read PDB files directly - either in PDB - format, or mmCIF. 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. -

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- 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 -

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- 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 - 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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- Switching between mmCIF and PDB format for - downloading files from the PDB
Jalview now employs the mmCIF format for importing 3D structure data - from flat file and EMBL-PDBe web-service, as recommended by the - wwwPDB. If you prefer (for any reason) to download data as PDB files - instead, then first close Jalview, and add the following line to - your .jalview_properties file:
- PDB_DOWNLOAD_FORMAT=PDB -
When this setting is configured, Jalview will only request - PDB format files from EMBL-EBI's PDBe.
mmCIF format - file support was added in Jalview 2.10. -

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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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