Viewing PDB Structures
+Jalview has a simple 3D structure viewer which can load PDB files and associate + the structure with a sequence in an alignment.
+There are 2 ways to load and associate a PDB file into Jalview application.
+Note the applet can only load PDB files by copying and pasting the text into + the popup window which appears when "Show PDB Structure" is selected + after right clicking on a sequence name.
+To see a particular structure, right click on a sequence name and from the + popup menu select "Sequence -> View PDB Entry".
+The PDB Structure viewer will perform a pairwise alignment of your sequence + and each PDB chain sequence. To view the results of the mapping, select "File + -> View Mapping" from the structure viewer window.
+Moving the mouse over the structure will highlight the residue in the alignment + window, and vice versa.
+Tips for Viewing Structures
+The "Connections" tab allows you to change the links made from Jalview - to your default web browser.
+The "Connections" tab allows you to change the links + made from Jalview to your default web browser.
URL Link From Sequence ID
Right click a sequence id to see a popup menu with "Link" as one of
the items. By default the item "SRS" is added to this link menu. This
@@ -49,15 +49,20 @@
box "Use a Proxy Server" and enter the address and port details as
necessary. Web Services will not work if you are using a proxy server and do
not enter the settings here.
The "Export" tab has a selection box allowing the user to set a default
- rendering style for EPS export. "Lineart" will produce an accurate
- representation of the visible alignment in Jalview, all the characters will
- be graphics objects. "Text" will produce a much smaller file and will
- rely on the software you use to view the EPS file, such as Adobe Illustrator,
- having the same font as the file was created with. You will only be able to
- edit text in an EPS file if you select the "Text" option.
+
The "Output" tab has a selection box allowing the
+ user to set a default rendering style for EPS export. "Lineart" will
+ produce an accurate representation of the visible alignment in Jalview, all
+ the characters will be graphics objects. "Text" will produce a much
+ smaller file and will rely on the software you use to view the EPS file, such
+ as Adobe Illustrator, having the same font as the file was created with. You
+ will only be able to edit text in an EPS file if you select the "Text"
+ option.
Choose "Prompt each time" to select between Lineart and Text each
time you make an EPS file.
The output tab also has a group of checkboxes for each file format. If these + are ticked, then Jalview will write files with the start and end sequence positions + appended to each sequence id. If the boxes are left unchecked for a paritcular + format, the sequence limits will not be appended to the sequence id.
View→Sequence Features
-When this option is selected, sequence features extracted from the - Uniprot record for each - sequence are displayed on the alignment.
-Currently, sequence features are rendered in red or blue, dependent - upon their type:
When this option is selected, sequence features extracted from the Uniprot + record for each sequence are displayed on the alignment.
+Jalview will attempt to retrieve sequence features from Uniprot files using + the EBI dbFetch web service using the given sequence names. A 100% match with + the Uniprot record is required to view the Sequence Features. If the match is + not 100%, Jalview will run EBI web service WUBlast to find unknown sequences. + You will be asked whether to proceed with this step, as it can take some time, + especially if the EBI servers are busy.
More information about the feature is given in a tooltip, which is viewed by moving the mouse pointer over a sequence feature. The description associated with the feature will then be displayed in a small label near the pointer.
-After the Sequence Features option is selected, there may be some delay before - the features are actually rendered, as jalview first determines if - the sequences are contained in Uniprot and then retrieves any sequence - records. This delay will normally only happen once for a particular - set of sequences, as jalview caches uniprot records in a file in your home - directory called '.jalview.uniprot.xml'. - -
The Sequence Identification Process +
View→Feature Settings... +
Once sequence features have been loaded onto an alignment features can be hidden
+ or have their rendering priority changed using the Feature Settings dialog.
+ This displays all the features loaded, the colour and whether to display the
+ feature or not. You can easily change the colour by clicking the colour box.
+ It is important to realise that the order in which features are drawn to the
+ alignment may result in overlapping features being hidden. Features at the foot
+ of the table are rendered first. Therefore features higher up the table will
+ be drawn over the top of lower featrues. You can change the order of the feature
+ priority by dragging the feature with your mouse.
+ Use the transparency setting as another way to visualise overlapping features.
+
You can save all features, with their current colours and visibility + in a Jalview format file. +
The Sequence Identification Process
The first step in the procedure for matching uniprot IDs to diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html new file mode 100755 index 0000000..02ff94e --- /dev/null +++ b/help/html/features/seqfetch.html @@ -0,0 +1,19 @@ + +
Sequence Fetcher
+The Sequence Fetcher can be started from the main desktop "File" + menu or from a particular alignment window.
+Select which database to fetch your sequence from and enter the sequence id. + If you are retrieving sequences from PDB database and you know which chain you + would like to retrieve, append the chain id after colon to the PDB id. eg 1GAQ:A
+The Sequence Fetcher uses WSDBFetch provided by the European Bioinformatics + Institute. If you use this service please quote:
+Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar
+ S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
+ SOAP-based services provided by the European Bioinformatics Institute.
+ Nucleic Acids Res. 33(1):W25-W28 (2005)
+
+
Exporting alignments as graphics and lineart
-The alignment view can be printed using -File→Print, or exported in a number of ways via the -File→Export menu: -
Tips for working with EPS Files
Exporting alignments as graphics and lineart
+The alignment view can be printed using +File→Print, or exported in a number of ways via the +File→Export menu: +
Tips for working with EPS Files
Each alignment, whether it is the original or an edited version may be saved in the standard formats using File→Save As
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
+Jalview will by default append the sequence start and end to each sequence name, +in the format /start-end. If you do not want this behaviour for a particular file +output, open the "Output" tab on the Preferences window where you can +select which file formats you want to append the start and end sequence positions +for.You can also save the current set of alignments and their colours, annotations and trees in a Jalview archive file using Desktop→Save project.
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index d66c14c..31b3f1f 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -31,12 +31,28 @@
Release |
New Features |
Issues Resolved |
2.07 + 7 /12/05 |
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2.06 28/9/05 |
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2.05b 15/9/05 |
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2.05 30/8/05 |
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2.04 24/8/05 |
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| 2.03 18/8/05 |
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| 2.02 18/7/05 |
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2.01 12/7/05 |
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| 2.0 20/6/05 |