: Editing pairwise sequence-structure alignments

Jul 1 2004

Contents


Introduction
Reference Guide
ICM command line options
Command line editing
Graphics controls
Editing pairwise sequence-structure alignments
Constants
Subsets and index expressions
Molecule intro
Selections
Arithmetics
Flow control
ICM molecular objects
Energy and Penalty Terms
Integer shell parameters.
Real shell variables
Logical variables
String variables
Preferences
Tables (structures)
Other shell variables
Commands
Functions
Macros
Files
User's guide
References
Glossary

Index

2.4 Editing pairwise sequence-structure alignments

ICM has a powerful editor for pairwise and multiple alignments. ICM alignment editor robust and safe. It protects you from unintended changes in the alignment. To edit an alignment one only needs four the types of operations:

select a block with one or several sequences to be moved (press Ctrl to add blocks). Important: since you can only move the selection to the gapped space , the moving front of the selection must be next to the gaps.
(optional) create space on both sides around a vertical section of the alignment
use the keyboard arrows to move the selected block with respect to the other sequences
squeeze out the excessive gaps (an item in the alignment popup menu)

OPERATION	KEYS
set a vertical selection for ALL sequences in the alignment	Double-Click
add white space by hitting the Space bar	SpaceBar
remove white space	Backspace
select a sub-block for shifting	Drag Left-Mouse-Button
shift the selected block next to a gapped area	Right and Left Arrows

Prev
gc2

Home
Up

Next
constant

Copyright© 1989-2004, Molsoft,LLC - All Rights Reserved.

This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.