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Last update on 25. Jun 2023 .
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SECEDIT display options


ARB_SECEDIT/Properties/Display options



Here you can change various options:

Display bases
Toggle display of bases
Distance between strands
Sets the distance between opposite helix strands (default=1)
Display bonds + Bond thickness
Select whether/how to display bonds. You can choose to display bonds for non-helical parts in the middle of a helix region by selecting '+Non-helix'. Click the 'DEFINE' button to specify bond-types and their layout (see ´SECEDIT bond definitions´). 'Bond thickness' defines the linewidth used to draw bonds.
Annotate cursor
Defines whether/how the current cursor position is annotated. If annotated, a small box containing a position number gets displayed.
  • None (=do not annotate cursor)
  • Absolute (=annotate with absolute alignment position)
  • Ecoli (=annotate with Ecoli-relative position)
  • Base (=annotate with base-number)

The positions used are the same as displayed in the ARB_EDIT4 top-area (see ´ARB_EDIT4 - Sequence primary and secondary structure editor´).
Annotate helices
If checked, each helix is annotated with its helix-number (as defined in SAI "HELIX_NR"; see ´Helix´).
Annotate ecoli positions
If checked, every 100th ecoli position is annotated.
Visualize search results
If checked, hits from ´Search and highlight sequence patterns´ get displayed in SECEDIT as well.
Visualize SAI
Toggle SAI visualization. See ´Visualize SAIs in editors.´.
Show all positions ...
Any position where the sequence of the currently ´Selected species´ has bases will always be displayed unconditionally. You can choose to additionally display
  • Binding helix positions
  • Ecoli base positions

Display Structure Skeleton + Skeleton thickness
Draw a skeleton of the secondary structure with variable line thickness.


Using the config-manager icon in the lower right corner of the window will also handle the settings made in the 'Bond definitions' subwindow.









No bugs known