Main Panel¶
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Control How Peak Symbols and Annotations Are Drawn
This popup window controls the display of picked peak positions within spectrum windows and also how their annotations are displayed in many of the tables throughout the rest of Analysis.
Peak Annotations
The “Annotation Style” tab, as the name suggests, controls which bits of information go to form the assignment annotation that is used to label peaks in spectra and when listing their identities in tables. The user can toggle various options on or off to dictate what should be included. With no options selected at all peaks will show only resonance number information like “[123],[45]”, irrespective of any atomic assignments. Switching the atom assignments on will substitute the atom and residue name for the resonance names. The spin system toggle is used to control the display of spin system numbers like the curly bracketed numbers of “{89}[123],[45]” or a residue name if the spin system is assigned, although the atom assignment option will also give any residue name. The chain and molecular system toggles are used when there are several sequences in the assignment that need to be distinguished, so that you can identify “A25LsyH,N” separately to “B25LysH,N” or even “MS2:A25LysH,N”. The details toggle allows the user to contribute to peak annotations; such details are set in the relevant column of the peak tables (e.g. Selected Peaks)or the “Peak::Set details” option of the right-click window menu. The last “Minimal Annotations” option is special because it gives a quick replacement for spectrum annotations that overrides all other settings, for example “25LysH,N” becomes “25K”, which is useful to reduce clutter when printing out an HSQC.
It should be noted that, with the exception of the “Minimal Annotations” option, any changes to the annotation options for existing peak assignments will not be visible until [Update Full Annotations] is pressed, which can take a while to update if the number of peaks in the project is large. Any new assignments will observe the current settings.
Draw Size
The second tab controls how the peak cross symbols, which indicate the pick position, are drawn in the spectrum display. Here, the user has four choices: the default is to use a fixed number of screen pixels, so that all symbols are the same size, irrespective of zoom level; uniform size in ppm (with the appropriate values for each isotope set in the lower table that appears) allows the peak symbol maintain a constant size relative to the contours, and thus differ in on-screen size according to the contour zoom level; and two choices for a “scaled” size where the peak symbol is larger or smaller depending on the intensity of the peak, either relative to its peak list or an absolute globally applied value.
Figure of Merit
The last “Merit Symbols” tab allows the user to add textual markers to a peak depending on the figure-of-merit value, which is an indication of reliability (although the precise context is at the discretion of the user). The merit value for a peak is set via the peak tables or the “Peak::Set merit” option of the right-click window menu. Aside from display purposes the merit value is used at a few points throughout Analysis to optionally exclude peaks. Typically a peak with a merit value of 0.0 may be ignored during certain analyses, e.g. for making NOE derived distance restraints.
Caveats & Tips
When assigning peaks via the Assignment Panel the resonance annotation will always display spin system information, given that this grouping is critical to assignment, but the chain and atom assignment will reflect the peak display, and thus these details may be missing if unset in this Draw Parameters popup.
Options specifying how peak annotations are drawn in spectrum windows and in tables etc.
Spin System Info: Whether to show unassigned spin system numbers like “{123}” in peak annotations; does not affect the display of full residue assignments
Atom Assignment: Whether to show assigned atom names in peak annotations rather than resonance numbers, e.g. “21LeuH,N” or “21Leu[55],[56]”
Chain Assignment: Whether to show the molecular chain code letter in peak annotations, e.g. “21LeuH,N” or “A21LeuH,N”
Molecular System: Whether to show the molecular system code name in peak annotations, e.g. “MS1:21LeuH,N” or “21LeuH,N”
Merit Symbol: Whether to show a symbol indicating the quality of a peak; these symbols must be set in the “Merit Symbols” tab
Details: Whether to show the details text for a peak in spectrum windows (set in the peak tables)
Minimal Annotations (overriding option): Whether to ignore above settings, and use a short peak annotation using only residue numbers and one-letter codes, e.g. “21L”
Update Full Annotations: Manually cause an update of all peak annotations; may take some time but recommended to see the immediate effect of changes
Options to specify how large the peak crosses/symbols are drawn in spectrum windows
*None*: Selects which mode to use for determining peak cross/symbol sizes; a fixed pixel/ppm value or scaled by intensity for all peaks or just one peak list
Enables the user to specify special symbols to annotate peaks according to quality
Good merit (>0.66): Although typically blank, sets a symbol to display for good quality peaks (merit value > 0.66), if the relevant option is selected in the “Annotation Style” tab
Medium merit: Sets a symbol to display for mediocre quality peaks (merit value between 0.34 & 0.66), if the relevant option is selected in the “Annotation Style” tab
Poor merit (<0.34): Sets a symbol to display for poor quality peaks (merit value < 0.34), if the relevant option is selected in the “Annotation Style” tab
Set symbols: Commit the changes to the merit symbols; this will not automatically update the display - see the “Annotation Style” tab