| More docs on the ARB website. See also index of helppages. Last update on 24. Jun 2017 .

Main topics:

- ARB_EDIT4 - Sequence primary and secondary structure editor

Related topics:

- Define Helix Symbols

# ARB_EDIT4 Options

- OCCURRENCE
- DESCRIPTION
- Online Sequence Compression
- Layout
- Scroll-Speed
- Editing
- EXAMPLES
- WARNINGS
- BUGS

## OCCURRENCE

### ARB_EDIT4/Properties/Options...

## DESCRIPTION

### This window allows you to adjust some display parameters

## Online Sequence Compression

### Online Sequence Compression (OSC) is a way to hide column positions (normally: column positions containing only or many gaps) in order to simplify editing of alignments with wide gaps.

### OSC affects only the manner how sequences are DISPLAYED in the editor and does not affect the sequences themselves.

### Available modes:

Show all gaps: Nothing is hidden.
Show some gaps: For each column range (consisting of gaps only) a different amount of gaps is shown, depending on the width of that column range. In detail:

    sequence has less than gaps    =>    display that many gaps
             100                                 G/10+1
             1000                                G/100+1
             else                                G/1000+1

Hide all gaps:
Hide no nucleotides: All column ranges consisting of gaps only are hidden.
Hide columns with less than X% nucleotides: This mode really makes nucleotides disappear from display. Use with care!
Those above mentioned column values are calculated on the basis of all sequences currently loaded in the editor.
Only sequence data is taken into respect while calculating gap positions. It is possible, that parts of a SAI get hidden by using OSC.

## Layout

### Sequence-helix spacing: Extra distance between sequence data and helix display (Default=0).

### Sequence-sequence spacing: Extra distance between two sequences (Default=0).

    Note: You may use negative values for the above settings to get a very compact
          display. Note that this will cause some minor drawbacks like cut-off
          underlengths (e.g. with small 'g') and character overlapping. Additional compaction
          is possible by switching off the helix display (see ´Define Helix Symbols´).

## Scroll-Speed

### Define the horizontal and vertical scroll speed for mouse scrolling (with middle mouse button). The default scroll-speed is 10/10, which scrolls with same speed as the mouse is moved.

### The display may also be scrolled using the mouse-wheel (optionally together with ALT/META).

## Editing

### Gap characters: set of characters which are handled as "gaps"

## EXAMPLES

### None

## WARNINGS

### None

## BUGS

### None