Peak : Draw Parameters

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.

Main Panel

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Annotation Style

Options specifying how peak annotations are drawn in spectrum windows and in tables etc.

check Spin System Info: Whether to show unassigned spin system numbers like “{123}” in peak annotations; does not affect the display of full residue assignments

check Atom Assignment: Whether to show assigned atom names in peak annotations rather than resonance numbers, e.g. “21LeuH,N” or “21Leu[55],[56]”

check Chain Assignment: Whether to show the molecular chain code letter in peak annotations, e.g. “21LeuH,N” or “A21LeuH,N”

check Molecular System: Whether to show the molecular system code name in peak annotations, e.g. “MS1:21LeuH,N” or “21LeuH,N”

check Merit Symbol: Whether to show a symbol indicating the quality of a peak; these symbols must be set in the “Merit Symbols” tab

check Details: Whether to show the details text for a peak in spectrum windows (set in the peak tables)

check 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”

button Update Full Annotations: Manually cause an update of all peak annotations; may take some time but recommended to see the immediate effect of changes

drawFrame

Options to specify how large the peak crosses/symbols are drawn in spectrum windows

pulldown *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

Merit Symbols

Enables the user to specify special symbols to annotate peaks according to quality

entry 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

entry 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

entry 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

button Set symbols: Commit the changes to the merit symbols; this will not automatically update the display - see the “Annotation Style” tab

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