ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Apr 24 2018

Contents
 
Introduction
Reference Guide
 ICM options
 Editing
 Graph.Controls
 Alignment Editor
 Constants
 Subsets
 Molecules
 Selections
 Fingerprints
 Regexp
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Arithmetics
 Flow control
 MolObjects
 Energy Terms
 Integers
 Reals
 Logicals
 Strings
 Preferences
 Tables
 Other
 Chemical
 Smiles
 Soap
 Gui programming
 Commands
 Functions
 Icm shell functions
 Macros
 Files
Command Line User's Guide
References
Glossary
 
Index
PrevICM Language Reference
Editing pairwise sequence-structure alignments
Next

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 to select a block next to a gap and move it with arrows. In total, there are four operations one might need:
  • 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


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