How do I use XRNA?
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.
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" .
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.
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.
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.
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.