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Contents
Contents
The manual
Version 3.5
©1997-2025 Luc Moulinier and CSTB
Complex Systems and Translational Bioinformatics,
The ICube laboratory
Centre de Recherches Biomédicales de Strasbourg (CRBS)
1, rue Eugène Boeckel
67 000 Strasbourg
FRANCE
Contents
1
Installing Ordalie
1
.
1
Requirements
1
.
2
Installation
1
.
2
.
1
Windows
1
.
2
.
2
Linux and Mac versions
2
Introduction
2
.
1
Context
2
.
2
Ordalie
3
Ordalie Basics
3
.
1
Alignments
3
.
2
Snapshots
3
.
3
Sequences names
3
.
4
Conventions
3
.
4
.
1
Mouse Buttons
3
.
4
.
2
Selections
3
.
4
.
2
.
1
Sequence names selections
3
.
4
.
2
.
2
Selecting a residue range
3
.
4
.
3
The database and the Ordalie file format
3
.
5
The Main Window
3
.
5
.
1
The Menus and the icons bar
3
.
5
.
2
The Snapshot bar
3
.
5
.
3
The Snapshot Frame
3
.
5
.
3
.
1
Sequence names
3
.
5
.
3
.
2
Amino acid sequences
3
.
5
.
3
.
3
Moving along the amino acid sequence
3
.
5
.
4
The Scores frame
3
.
5
.
5
The Control Panel
3
.
6
Features
4
Ordalie Tools
4
.
1
Snapshot Overview
4
.
1
.
1
The snapshot frame
4
.
1
.
2
Control panel
4
.
2
Editor
4
.
2
.
1
Control panel
4
.
2
.
1
.
1
Clear
4
.
2
.
1
.
2
Group
4
.
2
.
1
.
3
Ungroup
4
.
2
.
1
.
4
Lock/Unlock
4
.
2
.
1
.
5
Rem. Col. Gap.
4
.
2
.
1
.
6
Temp. Save
4
.
2
.
1
.
7
Save & Return
4
.
2
.
1
.
8
Cancel
4
.
2
.
2
Edition actions
4
.
3
The Identity tool
4
.
3
.
1
Control panel
4
.
3
.
1
.
1
Selection
4
.
3
.
1
.
2
Computation and Results
4
.
4
The Search motif tool
4
.
4
.
1
The search pattern syntax
4
.
4
.
2
Control panel
4
.
5
The Clustering tool
4
.
5
.
1
Criterions
4
.
5
.
2
Algorithms
4
.
5
.
3
Control panel
4
.
5
.
3
.
1
Selections
4
.
5
.
3
.
2
Clustering criterions
4
.
5
.
3
.
3
Clustering methods
4
.
5
.
3
.
4
Other buttons
4
.
6
The Tree tool
4
.
6
.
1
Control panel for tree building
4
.
6
.
1
.
1
Selections
4
.
6
.
1
.
2
Options
4
.
6
.
1
.
3
Draw / Return
4
.
6
.
2
The Tree window
4
.
6
.
2
.
1
The Drawing area
4
.
6
.
2
.
2
The Control panel
4
.
7
The Conservation tool
4
.
7
.
1
Methods
4
.
7
.
1
.
1
The 'Threshold' method
4
.
7
.
1
.
2
The automatic methods.
4
.
7
.
2
The Control panel
4
.
8
The Superposition tool
4
.
8
.
1
The superposition algorithm
4
.
8
.
2
Control panel
4
.
8
.
2
.
1
Selection
4
.
8
.
2
.
2
Control
4
.
8
.
3
Example : dealing with a homo-dimer.
4
.
8
.
3
.
1
Only one sequence chain present in the snapshot
4
.
8
.
3
.
2
Moving a dimer.
4
.
9
The 3D Viewer tool
4
.
9
.
1
Molecules and Objects
4
.
9
.
2
Representation types
4
.
9
.
3
The 3D Viewer window
4
.
9
.
3
.
1
Quick Mapping
4
.
9
.
3
.
2
Molecular Objects frame
4
.
9
.
3
.
3
The 3D window
4
.
9
.
3
.
4
The Actions panel
4
.
9
.
4
The Object Editor
4
.
9
.
4
.
1
Making / Editing an object
4
.
9
.
4
.
2
Residue selection
4
.
10
The Features Editor
4
.
10
.
1
Control panel
4
.
10
.
2
Notation and Actions
4
.
10
.
3
Contextual Menu
4
.
10
.
3
.
1
Select Item
4
.
10
.
3
.
2
Select All Items
4
.
10
.
3
.
3
Select Region
4
.
10
.
3
.
4
Clear Selection
4
.
10
.
3
.
5
Edit Item
4
.
10
.
3
.
6
Define New ...
4
.
10
.
3
.
7
Delete selected Items
4
.
10
.
3
.
8
Propagate Items to this group
4
.
10
.
3
.
9
Propagate Items to All
4
.
11
The Features Summary
4
.
11
.
1
Drawing Area
4
.
11
.
2
Control panel
4
.
12
The Annotation tool
4
.
12
.
1
Control Panel
4
.
12
.
2
Keyboard Bindings
4
.
13
Barcode
5
Menus Description
5
.
1
The File Menu
5
.
1
.
1
Open
5
.
1
.
2
Save
5
.
1
.
3
Save As ...
5
.
1
.
4
Save Window As
5
.
1
.
5
Close
5
.
1
.
6
Print
5
.
1
.
7
Quit Ordalie
5
.
2
The Edit Menu
5
.
2
.
1
Cut
5
.
2
.
2
Copy
5
.
2
.
3
Paste
5
.
2
.
4
Preferences
5
.
3
The View Menu
5
.
3
.
1
Bigger font
5
.
3
.
2
Smaller font
5
.
3
.
3
Open Log Console
5
.
3
.
4
Output Log as ...
5
.
3
.
5
Toggle Full Screen
5
.
3
.
6
Show/Hide Icon Bar
5
.
3
.
7
Show/Hide Scores
5
.
3
.
8
Show/Hide Features frame
5
.
3
.
9
Show/Hide Phylum
5
.
3
.
10
Show/Hide groups colours
5
.
3
.
11
Show/Hide sec. Str.
5
.
4
The Sequence Menu
5
.
4
.
1
Names as
5
.
4
.
2
Identity tool
5
.
4
.
3
Search motif
5
.
4
.
4
Retrieve Seq. Info.
5
.
4
.
5
Edit Info Seq
5
.
4
.
6
Features Editor
5
.
4
.
7
Add feature from file
5
.
4
.
8
Features Summary
5
.
4
.
9
Add in snapshot
5
.
5
The Alignment Menu
5
.
5
.
1
Editor
5
.
5
.
2
Re-Align sequences
5
.
5
.
3
Clustering
5
.
5
.
4
Add separator
5
.
5
.
5
Remove Separator
5
.
5
.
6
Remove All separators
5
.
5
.
7
Overview
5
.
5
.
8
Conservation
5
.
5
.
9
Tree building
5
.
5
.
10
Annotate snapshot
5
.
5
.
11
Barcode
5
.
5
.
12
Features Editor
5
.
5
.
13
Features Summary
5
.
5
.
14
Toggle physicochem. col.
5
.
6
The Structure Menu
5
.
6
.
1
Superpose Structures
5
.
6
.
2
Display Structures
5
.
6
.
3
Colour Sec. Str. by identity
5
.
6
.
4
Save PDB
5
.
7
The "?" Menu
5
.
7
.
1
About
5
.
8
Help
5
.
8
.
1
Local Ordalie documentation
5
.
8
.
2
On-line documentation
6
Appendix
6
.
1
The Ordalie database scheme
6
.
2
The FindPatterns syntax
6
.
2
.
1
Basic rules of syntax
6
.
2
.
2
Implied Sets and Repeat Counts
6
.
2
.
3
OR Matching
6
.
2
.
4
NOT Matching
6
.
2
.
5
Begin and End Constraints
6
.
3
The Vector Norm scoring method
6
.
4
The Feature File Format
6
.
5
The superposition algorithm
6
.
6
The command line options
Bibliography
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