How do I annotate a secondary structure graph?
Annotation refers to changing a nucleotides appearance (including
changing to a lower case letter, changing to a symbol, schematic,
etc.) and it refers to adding extraneous labels.
All annotation is done within the "Annotate" panel of XRNA.
- selecting a constrained region to annotate nucleotides with (see
How do I constrain effects of annotation
if changing a hairpin loop to be all triangles, then sel
- setting up a default label look by selecting in the left hand button panel
buttons that begin with "Default," like "Default Line."
Annotation of nucleotides is done by right clicking on a nucleotide character.
- To constrain effects of annotation of nucleotides use the pull down menu in
the upper "Main Controls:" panel of XRNA to select a constraint element. It should be initialized to "rna single nuc." When
a nucleotide letter is selected with either the left or right mouse button
then annotation will effect only nucleotides defined in the constrained region.
See Terminology used in XRNA to
determine what gets effected by a constrained region.
- To constrain effects of adding extraneous labels see What is the "Pick Strand" button in the "Main Controls:" panel for?
All extraeous labels are added in the "Annotate" panel. Adding extraneous labels involves
- selecting a constrained region to add labels to
(see What is the "Pick Strand" button in the "Main Controls:" panel for?)
- setting up a default label look by selecting in the left hand button panel
buttons that begin with "Default," like "Default Line."
- left mouse clicking on the scene for the approximate location
of a new label
- moving to the "Edit" panel at some point to position and alter.
- To undo a change to nucleotides, select a constrained region with the right mouse
button and select the "Clear Symbols" button.
- To undo adding an extraneous label right mouse click on the label and select the
"Delete" button.