Line List Window

This window displays the position, assignment and intensity of lines in the simulated spectrum. It appears when right-clicking on a peak in a simulated spectrum, and on each click all the lines close to the clicked position are added to this window, with the most intense first. You can adjust the number of lines added from the Line List Options Window. Simple line position fits can also be done directly from this window, though for anything other than the simplest of fits more the line lists are best placed in a text file as only limited editing is possible in the this window. (An initial text file can be created by copying and pasting from the line list window.) The contents of this window are normally (for version 5.2 and above) saved to and loaded from the .pgo file.

Click on an item in the picture below for more information:

Buttons

	Set frequency of selected lines from clipboard, assuming a number is available as text on the clipboard. The standard deviation is also set to 1. Measuring a peak by right clicking and dragging over a peak in an experimental or simulated spectrum in PGOPHER puts the peak position on the clipboard for this purpose. If the neighboring "Auto" item is checked (the default) this assignment is done automatically each time a peak in an experimental spectrum is measured. A blue line in the experimental spectrum will appear, indicating the measured peak position.
	If on, assign measured peak to selected transitions automatically (if off, this can be done manually using Assign).
	Show difference between first and last line selected.
	Select all lines in the line list window.
	Select no lines.
	Copy selected lines to clipboard and delete them.
	Copy selected lines to clipboard.
	Delete selected lines.
	Delete all lines.
	Delete unassigned lines, i.e. those with the standard deviation column empty.
	Menu for more actions: Save to File... - Save current lines to file in one of 4 formats (see the `Copy...` actions below), and set the resulting file as the current file in the Log Window. If the file already exists you are offered the option to append to the file rather than overwriting it. Sort On... - Sort lines by frequency, branch, upper or lower state quantum numbers, strength, width or standard deviation Copy Branch Table - Copy the lines in branch format to the clipboard. Copy Simple Format - Copy the lines as simple format linelist to the clipboard. This uses the comment field at the end of the line, so will not produce useful results in all cases. Copy BranchExpr Format - Copy the lines in BranchExpr format to the clipboard. Options - Bring up the Line List Options Window to change the options controlling the addition of lines to the line list.
	Plot assignments and display residuals
	Fit observations in this window, using the J, S (=symmetry) and # columns for the quantum numbers.
	Menu for more fit types: `Branch Fit` - Fit to the lines in this window, taking the quantum numbers from the branch label. `Simple Fit` - Fit to the lines in this window, taking the quantum numbers from the last column. Upper State CD Fit - Perform an upper state combination difference fit. Lines not part of a common difference are ignored. Lower State CD Fit - Perform a lower state combination difference fit. Lines not part of a common difference are ignored.
	Reset parameters to the value before the last fit cycle. This button is disabled until a fit has been done.

Column contents

Molecule	The molecule responsible for this transition.
M'	Manifold for the upper state of the transition
J'	Upper state total angular momentum or M'. (M' in the presence of static field, otherwise J' in the absence of hyperfine structure, otherwise F').
S'	Symmetry of the upper state.
#'	Eigenvalue number for upper state. This gives the index (starting from 1) of the upper energy level with respect to other levels of the same total angular momentum and symmetry.
M''	Manifold for the lower state of the transition
J''	Lower state total angular momentum or M". (M" in the presence of static field, otherwise J' in the absence of hyperfine structure, otherwise F').
S''	Symmetry of the lower state.
#''	Eigenvalue number for lower state. This gives the index (starting from 1) of the upper energy level with respect to other levels of the same total angular momentum and symmetry.
Position	The position of the transition; the units for this are the units used in the main simulation window. For line position fitting, alter this number to the position of the observed peak, either manually or (more usually) with the assignment process described under line position fits.
Std Dev	The (relative) standard deviation of this transition, used to calculate the weight of the observation in a line position fit. If this is negative, zero or blank this transition will not be included in the fit. Entries will initially have this blank or negative, and the automatic assignment process will set this to 1. Less certain measurements can be given larger values. Note that the parameters produced by a fit only depend on the relative values of the weights. If ShowEstUnc is set at the top level, then this column is set to the negative of the estimated uncertainty of the transition, based on the errors in the most recent fit, if available.
Strength	The intensity of the rotational transition.
Width	The width of the transition. (Note that this does not include the Gaussian or Lorentzian width set on the plot window.)
(Various)	The transition label in branch notation, such as P(1). The display will depend on the molecule type and the electronic and nuclear angular momenta included in the calculation. The example shown above is for an asymmetric top.
Name	Details of the transition, including other (possibly approximate) quantum numbers where appropriate. The assignment process will also add the source of the measurement (typically a filename) where possible.