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How do I use XRNA?
How stable is the current version of XRNA?
XRNA is currently offered as a beta version only. There is no guarantee of operation, smoothness of use, etc.

Do I ever need to cite a reference to XRNA?
No. There may be issues of using some labs, other than the Noller labs, determination of rna basepairing and/or general layout of a 2D structure graph. This is up to the user of XRNA to deal with.

How can I run a quick test?
For testing purposes go to the XRNA Gallery on the CMB-RNA web site and download a file to use as input for XRNA (currently only e.coli 5S is available and is called e.coli_5s.xrna).
Start up XRNA and read in the XRNA input file. This should display a secondary structure graph.

How do I read in a XRNA file?
With the XRNA "Choose File" button located in the "Import/Export" tab, browse to the xrna file and click on it, or type the xrna file name into the text field and click on "Open". All XRNA input/output file names end with the extension ".xrna" .

How do I read in an old style XRNA ".ss" input file?
Read in an old style, now deprecated, XRNA ".ss" input file like you would a new style XRNA input file. XRNA will not write out any changes made to a new .ss file, only a XRNA file. To initially change a XRNA session that was started with reading in a .ss file to a regular XRNA session go to the XRNA "Import/Export" tab and click the "Write XML" button. If you had read in a .ss file the prefix name should now appear with the extension ".xrna" and this will write out as a XRNA file.

How do I print using XRNA?
Go to the XRNA "Import/Export" tab and click the "Print" button. This will bring up a generic print window. XRNA generates postscript so the printer must be able to deal with postscript.

How do I print postscript to a file?
Go to the XRNA "Import/Export" tab and click the "Print" button. Click on the checkbox that says "Print to file," then click the "OK" button. This will bring up a text field to type in the postscript file name. After typing the file name then click the "OK" button. The postscript file should be in the directory that XRNA was started up in.

What is the "Pick Strand" button in the "Main Controls:" panel for?
Certain operations in XRNA require reference to a container. The best example is for adding extraneous labels to a figure. If the figure is one rna strand and that rna strand could be translated or added to a more complicated figure involving more than one rna strand, then these extraneous labels must be associated to either the rna strand, the rna strand container that the rna strand belongs to, or the entire scene. This allows for the translation of extraneous labels with the container selected. When selecting the "Pick Strand" button an inverted tree like structure of names will appear. The root of the tree is the entire scene. The next level of names will be rna strand groupings. The last level are leaves of the inverted tree and represent rna strands.

What is the terminology used in XRNA?

All terminology used in XRNA and the CMB-RNA XRNA faq and web pages, are for the creation, annotation and viewing of RNA secondary structure graphs created by XRNA only. The terminology may or may not have a counterpart in RNA 3D viewing programs or any other type of RNA software.
What is a secondary structure graph?
A secondary structure graph is the final visual output of XRNA. The output contains 1 or more rna strands each containing 1 or more nucleotides that may be base paired. The base pairing may occur across rna strands. The graph may also contain labels either specific to the nucleotides, rna strand, collection of rna strands or to the graph in general (see What is an extraneous label?).

What is a rna nucleotide?
A nucleotide is a nucleotide letter 'A', 'U', 'G', 'C', 'R', 'Y', 'N'. These letters are default for XRNA (and what are initially viewed) and will always be known by the program. To change the viewed nucleotide letter to something else (like the lowercase equivalent, or some kind of mutation symbol see the CMB-RNA XRNA faq for annotation.) A viewed nucleotide also implies a possible nucleotide number. This can be a line pointing from a nucleotide to a number or just a line. When editing and refering to a nucleotide a translation of a nucleotide will also translate its nucleotide number.

What is a rna single strand?
Refers to a single stranded region within a rna strand. A single stranded region is a contiguous set of nucleotides which contains no base pairs. For editing purposes, a single stranded region has 2 nucleotides that are considered the 5' and 3' ends of the single strand. These are called the single strand delineators. In a rna strand there are naturally occuring single strand delineators: When editing a secondary structure graph, delineators can be arbitrarily added to redefine the endpoints of a single stranded region. These delineators are only defined for the life of the editing session so care must be used in redefining arbitrary delineators on subsequent editing sessions. In this fashion single stranded regions can be easily edited to include arbitrary runs of straight lines and arcs.

What is a rna base pair?
Refers to 2 nucleotides base paired together. Any 2 nucleotide types can be base paired together. The most 5' nucleotide in a base pair is referred to as the 5' side of the base pair. The most 3' side is referred to as the 3' side of the base pair. The default viewing of base pairs is:
What is a rna helix?
What is a rna stacked helix?
First read the terminology for a rna cycle. A stacked helix is a run of helices, 5' to 3', connected by cycles that have 1 entry helix and 1 exit helix. In the e.coli 5S example the helices at 16, 18, 28, and 31 form a stacked helix. A stacked helix doesn't necessarily imply that they are visually aligned. A stacked helix may end in a hairpin loop helix.

What is a rna subdomain?
Refers to a rna helix and every nucleotide in the 5' direction from the end of the helix, 5' side, back to the end of the helix, 3' side.

What is a rna named group?
Similar to a "rna color unit" but nucleotides are grouped together by virtue of a common name. This is useful for the same reasons a "rna color unit" is and further for refering to commonly known "domains" in familiar secondary structure graphs like the 16S e.coli 5' domain.

What is a rna color unit?
Refers to a collection of nucleotides that can all be referred to at once by virtue of their visual color only. This is useful for the creation of complicated secondary structure graphs (like the group I Intron from the Cech lab) where there are many disjoint regions, arbitray groupings of structure, and mixtures of helices with both clockwise and counter-clockwise winding. A typical usage would be to annotate groups of nucleotides (using the standard grouping contraints) with some arbitrary but distinct color. One can then edit this similarily colored group of nucleotides as a unit.

What is a rna cycle? A cycle is a collection of helices, and their connecting single stranded regions, within a single rna strand that have the following definitions and relationships: The concept of a cycle is extremely useful during editing. A cycle is easily made circular. If it is circular then it can be interactively expanded or contracted maintaining the original helical angles. Also an exit helix and its subdomain can be edited such that it can move around the existing circle keeping an angle that is perpendicular to the circular cycle.

What is rna list nucs?
A way of referring to a collection of nucleotides that could be single stranded or base paired. 2 nucleotides are chosen in a rna strand as end points, inclusive, of the collection. The endpoints are chosen using the right mouse button only. After a nucleotide is chosen a properties menu will appear prompting to choose the next nucleotide. When the second nucleotide is chosen with the right mouse button then editing or annotating through the properties menu can commence.

What is a rna strand?
A contiguous set of nucleotides, numbered 1 -> N, that may have single stranded regions and base paired regions. The base paired regions may base pair with a different rna strand. The contiguous set of nucleotides may contain gaps in the numbering and still be considered a contiguous set.

What is a rna strand group?
Refers to a grouping of one or more rna strands.

What is labels only?
Sometimes used in editing if extraneous labels have been intermixed with rna structure. This allows one to pick only the labels and never pick structure.

What is the entire scene?
Refers to the entire scene in a secondary structure graph and is a container for "rna strand groups" and labels global to the whole scene. This concept is useful for edit and annotate commands that need to affect the entire scene.

What is a nucleotides ordinal value?
A nucleotide always belongs to a rna strand. The rna strand always starts its numbering from 1 and ends with the total number of nucleotides in the strand. The ordinal value of a nucleotide is therefore the number of the position in the strand that the nucleotide resides at.

What is a nucleotide label?
Any nucleotide can have a number next to it with a line pointing from the number to the nucleotide (alternatively, just the line pointing to the nucleotide). This number isn't necessarily the ordinal number of the nucleotide in its strand as sometimes it is useful to use a numbering system that is derived from a different strand. Typically every 10th nucleotide number in a secondary structure graph is labeled. Sometimes every 50th nucleotide is numbered while every 10th has a line next to it.

What is an extraneous label?
Any label that is not a nucleotide letter, nucleotide symbol, schematic, or nucleotide label. These can be text labels, arrows, circles, triangles, and parallelograms. There is an association that must be made between an extraneous label and the container in which it resides. This is important for any translation that is done on a container to also translate its extraneous labels. When adding an extraneous label check the "Main Panel:" button called "Pick Strand." See How do I use the Pick Strand button?' for details.

What is a hairpin loop?
Refers to the single stranded region at the end of a helix.

What is a connecting loop?
Any single stranded region that isn't a hairpin loop. This includes single stranded regions that connect helices (including a single "bulged" nucleotide) and the first and last contiguous sets of unbasepaired nucleotides in a rna strand. The term "loop" is still used no matter how the individual nucleotides are positioned in a single stranded region.

What is a helical axis? A 2d vector whose tail is at the midpoint of the starting base pair in a helix and whose head is at the midpoint of the end base pair in the same helix. The helical axis for a RNA stacked helix and for a RNA subDomain will be the helical axis of the starting helix in each.