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Features description

Since v.3.2
Add a static annotation
Shortcut: Ctrl+Shift+H
Popup-menu: Edit>Annotations>New>Here
Enabled when non "modifiable"? No
Creates and edits a static text annotation. An annotation is said to be static if its position does not depend on the position of any base. Static annotations can be selected and moved using the mouse.
Since v.3.6
Add base textual annotation
Shortcut:
Popup-menu: Edit>Annotations>New>Base
Enabled when non "modifiable"? No
Creates and edits a textual annotation anchored on and displayed on the side of the closest base.
Since v.3.6
Add chemical probing annotation
Shortcut:
Popup-menu: Edit>Annotations>New>Chem. Prob.
Enabled when non "modifiable"? No
Creates and edits a chemical probing type of annotation, targeting the closest couple of bases.
Since v.3.6
Add helix textual annotation
Shortcut:
Popup-menu: Edit>Annotations>New>Helix
Enabled when non "modifiable"? No
Creates and edits a textual annotation anchored on and displayed on the closest helix.
Since v.3.6
Add loop textual annotation
Shortcut:
Popup-menu: Edit>Annotations>New>Loop
Enabled when non "modifiable"? No
Creates and edits a textual annotation anchored on and displayed on the closest loop.
Since v.3.6
Add region highlight annotation
Shortcut:
Popup-menu: Edit>Annotations>New>Region
Enabled when non "modifiable"? No
Creates and edits an highlight annotation, based on the largest contiguous sequence of bases within current selection (or closest base if selection empty).
Since v.3.2
Align the exterior loop to a base line
Shortcut: Ctrl+F
Popup-menu: Edit>Redraw>Flat exterior loop
Enabled when non "modifiable"? No
In radiate drawing mode, redraws the whole structure, aligning to a baseline the base featured on the exterior loops (aka "dangling ends") .
Since v.3.2
Automatically annotate helices
Shortcut: Ctrl+Q
Popup-menu: Edit>Annotations>Auto helices
Enabled when non "modifiable"? No
Annotates each and every helix in the RNA with a unique "Hn" label.
Since v.3.2
Automatically annotate interior loops
Shortcut: Alt+Shift+Q
Popup-menu: Edit>Annotations>Auto interior loops
Enabled when non "modifiable"? No
Annotates each and every interior loop of the RNA with a unique "In" label.
Since v.3.2
Automatically annotate terminal loops
Shortcut: Ctrl+Shift+Q
Popup-menu: Edit>Annotations>Auto terminal loops
Enabled when non "modifiable"? No
Annotates each and every terminal loop of the RNA with a unique "Tn" label.
Since v.2.0
Choose backbone color
Shortcut: Ctrl+K
Popup-menu: Display>RNA Style>Backbone color
Enabled when non "modifiable"? No
Lets the user pick a custom color for rendering the phosphate-sugar backbone (aka skeleton) of the RNA.
Since v.2.0
Choose background color
Shortcut: Ctrl+G
Popup-menu: Display>Misc>Background color
Enabled when non "modifiable"? Yes
Defines the background color used within this panel.
Since v.3.0
Choose non-standard bases custom color
Shortcut: Ctrl+Shift+J
Popup-menu: Display>RNA Style>Non-standard bases>Color
Enabled when non "modifiable"? Yes
Defines and uses a special color to render non-standard bases (Anything but A,C,G or U)
Since v.1.0
Choose title color
Shortcut: Ctrl+Alt+T
Popup-menu: Display>Misc>Title>Color
Enabled when non "modifiable"? No
Selects the color used for rendering the panel title.
Since v.3.0
Customize border size
Shortcut: Ctrl+B
Popup-menu: Display>View>Border size
Enabled when non "modifiable"? Yes
Sets the width and height of the panel border, i.e. the gap between the panel boundaries and those of the surface used to draw the RNA.
Since v.3.0
Customize colors (All)
Shortcut: Alt+U
Popup-menu: Edit>Colors>By position
Enabled when non "modifiable"? No
Lets the user select custom colors (inner, outer, label...) for each base, selected by base numbers.
Since v.3.0
Customize colors (By base type)
Shortcut: Ctrl+U
Popup-menu: Edit>Colors>By base
Enabled when non "modifiable"? No
Lets the user select custom colors (inner, outer, label...) for each type of base. One can then set the colors of a bunch of bases in a single operation.
Since v.3.0
Customize colors (By base-pair)
Shortcut: Shift+U
Popup-menu: Edit>Colors>By BP
Enabled when non "modifiable"? No
Lets the user select custom colors (inner, outer, label...) for each type of base-pair. One can then set the colors of a bunch of bases in a single operation.
Since v.3.0
Define "Gaps" bases color
Shortcut: Ctrl+Shift+D
Popup-menu: Display>RNA Style>'Gaps' bases>Color
Enabled when non "modifiable"? No
Defines and uses a special color to draw "Gaps" bases in comparison mode. "Gaps" bases correspond to insertion/deletions in one of the structures.
Since v.3.2
Edit annotations from list
Shortcut:
Popup-menu: Edit>Annotations>Edit from list...
Enabled when non "modifiable"? No
Spawns a complete list of annotations, allowing for a quick edition of all text annotations.
Since v.3.2
Edit/annotate all bases of an RNA
Shortcut:
Popup-menu: Edit>Selection>All
Enabled when non "modifiable"? No
Pops up a menu allowing for a simultaneous customization of all of the bases comprised between the selected base and all terminal loops. Available options are exactly the same as for single bases and are applied to all of the bases in the loop at once, except for annotations which is not available for this selection.
Since v.3.2
Edit/annotate all bases of the closest helix
Shortcut:
Popup-menu: Edit>Selection>Helix
Enabled when non "modifiable"? No
Pops up a menu allowing for a customization of how all of the bases involved in the helix containing the selected base-pair are to be rendered. Available options are exactly the same as for single bases and are applied to all of the bases in the loop at once, except for annotations. In case of an annotation, the text is displayed only once on the barycenter of the bases involved in the helix.
Since v.3.2
Edit/annotate all bases of the closest loop
Shortcut:
Popup-menu: Edit>Selection>Loop
Enabled when non "modifiable"? No
Pops up a menu allowing for a customization of how all of the bases involved in a loop containing the selected base are to be rendered. Available options are exactly the same as for single bases and are applied to all of the bases in the loop at once. If the selected base is involved in a basepair, then there is ambiguity as to which loop the user wants to apply the modifications to. In this case, two options "Forward loop"/"Backward loop" replace the classic "Loop", with the "Backward loop" being the closest to the 5'/3' dangling end. In case of an annotation, the text is displayed only once on the barycenter of the bases involved in the loop.
Since v.3.2
Edit/annotate all bases of the closest stem
Shortcut:
Popup-menu: Edit>Selection>Stem
Enabled when non "modifiable"? No
Pops up a menu allowing for a simultaneous customization of all of the bases comprised between the selected base and all terminal loops. Available options are exactly the same as for single bases and are applied to all of the bases in the loop at once, except for annotations which is not available for this selection.
Since v.3.2
Edit/annotate all bases of the closest unpaired region/bulge
Shortcut:
Popup-menu: Edit>Selection>Bulge
Enabled when non "modifiable"? No
Pops up a menu allowing for a customization of how all of the unpaired bases contiguous to the selected base-pair are to be rendered. Available options are exactly the same as for single bases and are applied to all of the bases in the loop at once, except for annotations which are not available.
Since v.3.2
Edit/annotate both bases of the closest base-pair
Shortcut:
Popup-menu: Edit>Selection>Base-pair
Enabled when non "modifiable"? No
Pops up a menu allowing for a customization of how both of the bases involved in the closest base-pair are to be rendered. Available options are exactly the same as for single bases minus text annotations.
Since v.3.2
Edit/annotate closest base
Shortcut:
Popup-menu: Edit>Selection>Base
Enabled when non "modifiable"? No
Pops up a submenu allowing for a customization of how this single base is rendered. More specifically, it is possible to:
  • Set the base content (amino-acid)
  • Change the color used to fill this base
  • Change outline color
  • Change caption color
  • If involved in a base-pair, change base-pair color/thickness
  • Change base number color
  • Add/edit/remove a text annotation for this base.
Note: For single bases, annotations are drawn on the side of the base, using a similar approach as the one used for base numbers.
Since v.3.6
Edit/annotate current selection
Shortcut:
Popup-menu: Edit>Selection>Current
Enabled when non "modifiable"? No
Pops up a submenu allowing for a customization of how selected base are rendered.
Since v.2.0
Export picture
Shortcut: Ctrl+X
Popup-menu: File>Export
Enabled when non "modifiable"? Yes
Exports the current image of the RNA in one of supported formats. As of version 3.1, Encapsulated Postscript (EPS), Scalable Vector Graphics (SVG), XFIG, Portable Network Graphics (PNG) and JPEG are supported for export. Some formats might require additional parameters such as quality and/or resolution (pixel-based graphics).
Since v.3.0
Learn more about VARNA
Shortcut: Ctrl+A
Popup-menu: About
Enabled when non "modifiable"? Yes
Spawns a dialog featuring current version, licence status, current contributors and funding institution.
Since v.3.0
Manual input of an RNA
Shortcut: Ctrl+N
Popup-menu: File>New...
Enabled when non "modifiable"? No
Allow the user to manually input a structure/sequence of RNA using the dot-bracket notation. The structure is then rendering using the current algorithm/settings.
Since v.3.0
Open new file
Shortcut: Ctrl+O
Popup-menu: File>Open...
Enabled when non "modifiable"? No
Opens a file containing an RNA description. The file content is matched against the four file formats supported for input (Vienna, CT, BPSeq and RNAML), and the RNA is drawn using current settings and algorithm.
Since v.3.6
Print current view
Shortcut: Ctrl+P
Popup-menu: File>Print...
Enabled when non "modifiable"? Yes
Outputs to printer current RNA secondary structure.
Since v.3.7
Read color map values from file
Shortcut: Ctrl+Shift+K
Popup-menu: Display>Color Map>Load values...
Enabled when non "modifiable"? No
Loads a list of values from an external file/URL.
Since v.2.0
Redraw in Circular mode
Shortcut: Ctrl+2
Popup-menu: Edit>Redraw>Algorithm>Circular
Enabled when non "modifiable"? No
Redraws the current RNA secondary structure using the circular "Feynman's diagram" representation.
Since v.2.0
Redraw in Linear mode
Shortcut: Ctrl+1
Popup-menu: Edit>Redraw>Algorithm>Linear
Enabled when non "modifiable"? No
Redraws the current RNA secondary structure using the linear representation.
Since v.2.0
Redraw in NAView mode
Shortcut: Ctrl+4
Popup-menu: Edit>Redraw>Algorithm>NAView
Enabled when non "modifiable"? No
Redraws the current RNA secondary structure in a planar representation, using the NAView algorithm.
Since v.2.0
Redraw in Radiate mode
Shortcut: Ctrl+3
Popup-menu: Edit>Redraw>Algorithm>Radiate
Enabled when non "modifiable"? No
Redraws the current RNA secondary structure using the "radiate" planar representation. Using the mouse, helices can be spined around for aesthetic purpose.
Since v.3.2
Remove annotations from list
Shortcut:
Popup-menu: Edit>Annotations>Remove from list...
Enabled when non "modifiable"? No
Spawns a complete list of annotations, allowing for a quick deletion of numerous annotations.
Since v.3.1
Reset drawing
Shortcut: Ctrl+Shift+R
Popup-menu: Edit>Redraw>Reset
Enabled when non "modifiable"? No
Lets the user cancel any changes performed on the structure since the initial drawing.
Since v.3.0
Rotate RNA
Shortcut: Ctrl+R
Popup-menu: Display>View>Rotation...
Enabled when non "modifiable"? No
Rotates the whole RNA of a certain angular increment. (Doesn't rotate the captions)
Since v.2.0
Save RNA structure
Shortcut: Ctrl+S
Popup-menu: File>Save...
Enabled when non "modifiable"? Yes
Saves the displayed RNA secondary structure using one of the supported formats (As of version 3.1: Vienna DBN, connect CT and CRW BPSeq).
Since v.1.0
Select title font size
Shortcut: Ctrl+Shift+T
Popup-menu: Display>Misc>Title>Font
Enabled when non "modifiable"? No
Lets the user select the font family, style and size used for displaying the title.
Since v.3.0
Set BP increment in linear mode
Shortcut: Ctrl+H
Popup-menu: Edit>Redraw>BP height increment
Enabled when non "modifiable"? No
In linear drawing mode, defines the vertical increment used to separate two successive, nested base-pairs.
Since v.3.0
Set base-pairs display style
Shortcut: Ctrl+Shift+P
Popup-menu: Display>RNA Style>Base pairs>Base-pairs style...
Enabled when non "modifiable"? Yes
Lets the user picks his/her favorite style for base-pairs rendering, chosen among:
  • none, base-pairs are not drawn, but can be implicitly seen from "ladders", ie helix structures
  • line (Line), a simple line is used to draw any base-pair, regardless of its type
  • rnaviz, a small square is drawn at equal distance of the two partners
  • lw (Leontis/Westhof), both canonical and non-canonical base-pairs are rendered according to the Leontis/Westhof nomenclature.
Since v.3.4
Set color map caption
Shortcut: Ctrl+Shift+C
Popup-menu: Display>Color Map>Caption
Enabled when non "modifiable"? No
Sets the caption of current color map. Setting the caption to the empty strings hides the color map caption (ie no space is used for the caption).
Since v.3.4
Set color map palette
Shortcut: Ctrl+L
Popup-menu: Display>Color Map>Style...
Enabled when non "modifiable"? No
Sets the color map palette to be used within a color map drawing. One can either choose a predefined palette of define a custom palette. Predefined palettes are: "red", "blue", "green", "heat", "energy", and "bw". A custom palette is defined as a semi-colon-separated sequence of (value/rgb color) couples (e.g. "0:#000000;1:#FFFFFF" for a black to white color map). The colors are obtained from a set of values through linear interpolations on each RGB component. For instance, a custom map "0:#000000;1:#808080" going from black (#000000) to gray (#808080) will assign a dark gray color (#404040) to a base of value "0.5". Also, the color map range is automatically scaled as to match the range of base values, so it should not be necessary to manually account for the range.
Since v.3.4
Set color map values
Shortcut: Shift+L
Popup-menu: Display>Color Map>Edit values...
Enabled when non "modifiable"? No
Assigns a list of real values, used for color map rendering, to the bases of an RNA. The values are assigned sequentially in the 5' to 3' order. If list is shorter than the list of bases, the remaining bases will remain unaffected. Default value for each base is 0.0.
Since v.3.0
Set inter-base distance factor
Shortcut: Ctrl+Shift+S
Popup-menu: Edit>Redraw>Space between bases
Enabled when non "modifiable"? No
Lets the user define the multiplier used for inter-base distance. Since the applet adapts it zoom factor to the dimension of the RNA bounding box, this option might be mistaken for a increase of the base radius.
Since v.2.0
Set numbering period
Shortcut: Ctrl+M
Popup-menu: Display>Misc>Num. periodicity
Enabled when non "modifiable"? Yes
Sets the interval between two successive base numbers. More specifically, if k is the period, then the first and last bases of the RNA are numbered, along with each base whose number is a multiple of k. The base number is used for this operation as opposed to the base index, which might differ if bases are missing in the RNA.
Since v.2.0
Set title
Shortcut: Ctrl+T
Popup-menu: Display>Misc>Title>Set title...
Enabled when non "modifiable"? No
Lets the user type a new title, displayed on the bottom of the panel.
Since v.3.0
Set zoom level
Shortcut: Ctrl+Z
Popup-menu: Display>View>Zoom
Enabled when non "modifiable"? Yes
Defines the level of zoom and zoom increment used to display the RNA within this panel. For zoom levels greater than one, the arrows or the mouse (middle button or both button simultaneously) can be used to scroll visible portion.
Since v.3.4
Toggle color map view
Shortcut: Ctrl+Shift+L
Popup-menu: Display>Color Map>Show color map
Enabled when non "modifiable"? No
Sets the caption of current color map. Setting the caption to the empty strings hides the color map caption (ie no space is used for the caption).
Since v.3.0
Toggle non-canonical base-pairs display
Shortcut: Ctrl+W
Popup-menu: Display>RNA Style>Base pairs>Show non-canonical BPs
Enabled when non "modifiable"? No
Switches on/off the display of non-canonical base-pairs.
Since v.3.0
Toggle non-planar portions (pseudoknots) display
Shortcut: Ctrl+E
Popup-menu: Display>RNA Style>Base pairs>Hide tertiary base-pairs
Enabled when non "modifiable"? No
Toggles on/off display of "non-planar" base-pairs, i.e. pseudoknots. Since there is no canonical definition of pseudoknotted portions, a maximal planar subset is extracted from the input structure, defined to be the planar portion, and used as a scaffold for the drawing algorithms. The remaining base-pairs can either be displayed or not with this option.
Since v.3.0
Toggle on/off custom color for non-standard base
Shortcut: Ctrl+J
Popup-menu: Display>RNA Style>Non-standard bases>Custom colored
Enabled when non "modifiable"? Yes
Toggles on and off using a custom color for rendering non-standard base pairs (Anything but A,C,G or U).
Since v.3.9
Toggle show/hide base outlines and fillings (formerly known as "Gaspin/Gautheret" mode)
Shortcut: Alt+G
Popup-menu: Display>RNA Style>Non-standard bases>Toggle draw bases
Enabled when non "modifiable"? Yes
Toggles on/off the display of circles around bases (i.e. "Vienna style"-like). Thanks for Christine Gaspin and Daniel Gautheret for suggesting this popular feature.
Since v.3.0
Toggle using custom color for "Gaps"
Shortcut: Ctrl+D
Popup-menu: Display>RNA Style>'Gaps' bases>Custom colored
Enabled when non "modifiable"? Yes
Toggles on/off using a special color to draw "Gaps" bases in comparison mode.
Since v.2.0
Zoom in
Shortcut: +
Popup-menu:
Enabled when non "modifiable"? Yes
Zooms in on the center of the currently drawn RNA
Since v.2.0
Zoom out
Shortcut: -
Popup-menu:
Enabled when non "modifiable"? Yes
Zooms out on the center of the currently drawn RNA

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