How do I edit a secondary structure graph?

• How do I constrain effects of editing?
• How do I edit stuff according to constraints?
• What are the details for editing with the left mouse button?
• What are the details for editing with the right mouse button?
• How do I add/delete nucleotide labels?
• How do I edit nucleotide labels or any other extraneous label?
• How do I undo an edit?
• How do I unset base pairs?

How do I constrain effects of editing?

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 the constraints are shown in green. Editing will be done only on nucleotide letters shown in green. See Terminology used in XRNA to determine what gets effected by a constrained region.

How do I edit stuff according to constraints?

In general a constrained element can edited (moved or rotated) by using the left mouse button in a kind of immediate edit mode, or the right mouse button that brings up a properties menu to allow for editing.

To edit with the left mouse button select the "edit" radio button on the left hand panel. Select a nucleotide letter with the mouse. While holding the left mouse button down move the mouse until desired location and release the mouse button. Once a constrained element is highlighted in green (and the mouse focus has remained in the editing area) it may be moved with the arrow keys on the keyboard rather than with the mouse.

Alternatively use the edit properties menu for a constrained element by selecting a nucleotide letter with the right mouse button and using appropriate buttons or text fields to edit nucleotides in a constrained region. The properties menu for each constrained type will have at least 3 buttons in common:

• Nuc Labels - This button brings up a panel of commands for adding and deleting nucleotide labels from a constrained grouping of nucleotides.
• Set Hidden Attributes - Clears the scene of all nucletides in a constrained grouping. This is useful during editing when too many connecting single strand regions are confusing the scene.
• Add to Group Named: - Adds current constrained region to the grouping named in the corresonding text field.

What are the details for editing with the left mouse button?

First read the CMB-RNA XRNA Faq question How do I edit stuff according to constraints? Further details of editing constrained regions with the left mouse button follow (see XRNA Terminology for a general explanation of constrained region types):

• RNA Single Nuc - Can only move a non basepaired nuc. Use editing or formatting a base pair to change a nucleotides position in a base pair.
• RNA Single Strand - Edit a single stranded region of nucleotides. See What is a rna single strand? to understand the concept of a rna single stranded regions delineators. To set an arbitrary delineator: while in the "Edit" panel in RNA Single Nuc constraint mode, right mouse select a non base paired nucleotide in the single stranded region to be affected and set the radio button labeled "set to Single Strand delineator." If the single stranded region is anything but a straight line of nucleotides then editing will be done in an arced mode (The delineated nucleotides are considered in the figuring of an arced region so it could be the case that a straight line of nucleotides will be treated as an arced region). If the single strand is a straight line of nucleotides then editing will be done in a straight line mode. To insure that an arc is treated as a straight line choose in the left hand panel the radio button entitled "Always format Single Strands straight." To make a straight line arced simply move one nucleotide out of position in "single nuc mode" and edit in "single strand mode." Alternatively, change back and forth between straight and arced by right mouse clicking on a nucleotide (see What are the details for editing with the right mouse button? under RNA Single Strand). Editing complicated single stranded regions consisting of many runs of straight lines and arced regions is simple if you plan ahead and set arbitrary delineators correctly.
  • To edit an arced region: select a nucleotide letter somewhere in the middle of the arced region. While holding the left mouse button down move the mouse approximately in a direction perpendicular to a line that is made up by the end points of an arced region. The nucleotides that will arc are colored green with the endpoints of the arced region nucleotides colored red and remaining stationary. Alternatively, once an arced region has been selected the up arrow key will make the arc bigger while the down arrow key will make it smaller.
  • To edit a straight line region: selecting a nucleotide letter somewhere in the middle of the straight line region will cause the straight single strand region to move as a whole. Selecting a nucleotide letter somewhere towards either end point of the single strand will cause movement from that endpoint while having the other endpoint anchored. Alternatively, once selected a straight line can be moved around with the arrow keys.
  • To edit an arced region within single stranded regions simply edit the arced region as usual.
  • To edit a straight region within other straight regions it is often the case that the editor will determine that you are editing in arced mode since one nucleotide may be out of line (an arbitrary delineator of one line can be shared with another, therefore one of the lines might contain a nucleotide that isn't in a straight line). This can be of considerable nuisance so select the button on the left hand panel of the "Edit" Panel entitled "Always edit single strands straight."
• RNA Basepair - there is no editing allowed to a basepair with the left mouse button. To reformat a basepair see the CMB-RNA XRNA faq on using the "Format" panel in XRNA. Occasionally one must deal with a single base pair that isn't contiguous to any other base pairs in a helix. This would be a helix of length 1. Use right mouse button editing for this.
• RNA Helix - Select any nucleotide in a helix and move. To rotate hold the Shift-Key down while moving the mouse. This will cause a rotation around the mid-point of the start of the helix. The angle of the helix can be fine tuned by right mouse clicking on the helix and using the RNA Helix properties menu. This is the preferred method of rotating a helix. If instead of selecting the "edit" radio button in the Edit panel the "move along helical axis" radio button is selected then when a helix is picked with the left mouse button and the arrow keys are used for editing the translation will only occur along the helical axis.
• RNA Stacked Helix - Same as RNA Helix
• RNA SubDomain - Same as RNA Helix. Using the "move along helical axis" radio button and editing with arrow keys is especially useful here for moving helical elements of a stacked helix along the helical axis.
• RNA Named Group - pick any nucleotide. All nucleotides that have been grouped together by a common name will move. This especially useful for editing complicated scenes, like a group I Intron, that have discontinuous regions.
• RNA Cycle - There is no concept of moving a cycle. Use the constraint mode of RNA SubDomain to move instead.
• RNA Color Unit - pick any nucleotide. All nucleotides that have been colored with the same color, using the XRNA "Annotate" panel, will move. This especially useful for editing complicated scenes, like a group I Intron, that have discontinuous regions. Once a grouping of helices and single stranded regions has been established then it is easy to use the "Annotate" panel to color all nucleotides using standard constraining, like with RNA List Nucs.
• RNA List Nucs - used only with right mouse click property menus.
• RNA Strand - pick any nucleotide to move the whole rna strand that the nucleotide belongs to.
• RNA Strand Group - if working with a grouping of 2 or more rna strands then picking a nucleotide and moving the mouse will move the entire grouping.
• Labels only - move only non-nucleotide labels. This is useful if trying to pick a label that is too close to nucleotides to safely not pick a nucleotide.
• Entire Scene - Only used with right mouse properties menu.

What are the details for editing with the right mouse button?

First read the CMB-RNA XRNA Faq question How do I edit stuff according to constraints? Translate any constrained region that can be translated by using the "Center X,Y" textfields and buttons. Rotate any constrained region that can be rotated by using the "angle" textfields and buttons. Add nucleotide labels by using the "Nuc Labels" button. Further details of editing constrained regions with the right mouse button follow (see XRNA Terminology for a general explanation of constrained region types):

• RNA Single Nucleotide - The "Nuc Labels" button will only affect this single nuc and the nucleotide label number will be initialized to the ordinal number value of this nucleotide. This properties menu is where one sets a non base paired nucleotide as an arbitrary single strand delineator by selecting the radio button entitled "set to Single Strand delineator."
• RNA Single Strand - Divided into two parts:
  • Arced
    • The button named "Readjust arc in place" will take an existing arc, not necessarily well formed, and try make a closest fit arc to it.
    • The button named "Readjust arc to default" will make an initial arc to be further edited.
    • Use the "flip" button to make an arc go to the other side of its delineators.
  • Straight line
    • The button named "Readjust Nuc Line" will make a best straight line of nucleotides between the single strand delineators.
    • Use the text fields called "5'->3' angle" and "nuc->nuc+1 distance" to make a straight line of nucleotides with the 5' end fixed, the 3' end off at specified angle and each nucleotide spaced the specified amount apart.
    • move the 3' or 5' ends by selecting appropriate radio button, or the entire line by using the "mid" radio button, and the arrow keys supplied.
• RNA Cycle - First understand a rna cycle by reading What is a rna cycle? When editing an rna cycle the entry helix will be shown in red and everything else that can be affected by an edit is shown in green. Sometimes it is desirable for all helices to be situated around a circle with the helices perpendicular to the circle. Other times it is desirable to leave the angle and positions of the helices alone and just affect the connecting single stranded regions. The editing that can be done with a rna cycle is:
  • Press the "Reset Cycle" button to get a new initial conformation. This will try and figure out a best circle to place helices and their connecting single strands.
  • Change the radius of the cycle circle by using the "Cycle Radius" panel. This will reset any helices to a new angle by trying to make a best circle.
  • Move an exit helix around the cycle circle by selecting the exit helix in question while selecting the cycle. This exit helix can then be rotated around the current cycle circle by using the "helix angle" buttons. If the current cycle circle isn't really a circle then unexpected results can occur. Start by using the "Reset Cycle" button and the "Cycle Radius" panel if this is the case.
  • Hide connecting single stranded regions. This is useful when trying to edit helices in a non circular cycle and the single stranded regions are in the way.
  • After reshowing hidden connecting single stranded regions that were hidden while editing exit helices, they may be out of place enough to use the "Reset single strands" button. This will try and make a best circular conformation with the connecting single stranded regions of a cycle.
• Entire Scene - This is the only constraint where the background of the scene is picked with the right mouse button rather than a nucleotide. Commands found here effect the entire scene or will effect all nucleotides in all rna strands.

How do I undo an edit?

How do I unset base pairs?

How do I add/delete nucleotide labels?

• Select Font - The font for a nucleotide label will try to be construed by looking at any existing nucleotide labels in the rna strand that the nucleotide resides in. If no nucleotides in a rna strand have a label then the font type: "Helvetica-PLAIN", point size 8, will be used. If this needs to be overwritten then the "Select Font" button will provide a way of choosing a different font.
• Add Nuc Labels -
  • Nucleotide labels will be added to nucleotides, in a constrained collection only, with an ordinal value that is modulus 10.
  • If the constrained collection is a single rna nucleotide then a nucleotide label will always be added.
  • To add nucleotides to every 10th nucleotide in every rna strand in a scene use the constrained collection type "Entire Scene."
  • Adding nucleotide labels to nucleotides that already have a label won't work. Delete the nucleotide labels first.
  • Editing of nucleotide labels is often necessary and can be done by left or right mouse button clicking on the line or number label. See details of editing labels elsewhere in the XRNA Faq.
  • The length of generated nucleotide labels lines can be set only globally through the Entire Scene properties menu in the text field labeled "nuc line length."
• Delete Nuc Labels - Delete any nucleotide labels in a constrained region, if any, before attempting to add.

How do I edit nucleotide labels or any other extraneous label?