ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Jun 5 2024

Reference Guide
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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 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)

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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