This document is for OpenStructure version 1.4, the latest version is 2.9.0 !

The Sequence Viewer

The sequence viewer of OpenStructure can be used to display sequences or alignments.

The following example adds an alignment to a sequence viewer and shows it in a new sequence viewer instance:

aln=io.LoadAlignment('sh2.aln')
v=gui.SequenceViewer()
v.AddAlignment(aln)
v.Show()

Core Features

Display styles

It is possible to display the data in different ways. To change the display style, click the tool icon of the menubar and select the display style from the list.

../../_images/100615_select_display_style.png

For the moment there are four different display styles:

1. Highlight propteries

../../_images/100615_property_type.png

Color groups of amino acids

grey orange yellow green red blue cyan
G F C S K D P
A Y M T R E  
V W     H N  
L         Q  
I            

2. Secondary structure

../../_images/100615_secondary_structure.png

Display secondary structure information

This mode is only available, when a mol.EntityView is connected to the sequence.

3. Highlight conservation 1

../../_images/100615_conservation_1.png

Display conservation

This display style uses the seq.alg.Conservation()-Algorithm which calculates the Conservation for each column. This Mode is only available for alignments.

4. Highlight conservation 2

../../_images/100615_conservation_2.png

Display conservation

This implementation of conservation colors the columns grey, if all amino acids are from the same type. If all amino acids are from the same group, it colors the column with a light grey. Otherwise the column is colored white. This Mode is also only available for alignments.

Zoom

With the sequence viewer of Openstructure it is possible to zoom in and out <ctrl + mousewheel>.

../../_images/100616_zoom_in.png

Zoom in, if you lost your glasses at home

../../_images/100616_zoom_out.png

Zoom out, if you need a better overview of the sequence

Copy and Paste

It is possible to copy sequence text from the sequence viewer by pressing <ctrl + c>. If you paste the text (for example into a text editor), all the gaps will be filled with -.

../../_images/100616_copy_paste.png

Search

Enter search terms or a module, class or function name.

Contents

Documentation is available for the following OpenStructure versions:

dev / 2.9.0 / 2.8 / 2.7 / 2.6 / 2.5 / 2.4 / 2.3.1 / 2.3 / 2.2 / 2.1 / 2.0 / 1.9 / 1.8 / 1.7.1 / 1.7 / 1.6 / 1.5 / (Currently viewing 1.4) / 1.3 / 1.2 / 1.11 / 1.10 / 1.1

This documentation is still under heavy development!
If something is missing or if you need the C++ API description in doxygen style, check our old documentation for further information.