nv_peak: Use this command to interact with peak lists. Many commands refer to the "active list". This is the list that is currently selected in the "PEAK ANALYSIS PANEL".
nv_peak add ? LIST?: Adds a entry for a peak to the end of the peak list, and returns the new peaks number. The peak list examined is the active list if "LIST" argument is not specified, otherwise the specified list is examined. Sets peak position, width etc. of the new nv_peak to zero.
nv_peak closest ? LIST?: Returns the number of the peak closest to the cursor. The peak list examined is the active list if "LIST" argument is not specified, otherwise the specified list is examined. Note: the peak located will be closest to the cursor position, not the mouse position. For example, peak closest noesy, would find the peak in the peak list named "noesy", that is closest to the cursor position. If no peak is within a certain tolerance, an error message will be returned.
nv_peak cluster ? LIST1 LIST2 ...?: This command clusters together the peaks in one or more peak lists. Lists can be clustered based on the chemical shifts in one or more dimensions. The dimensions and tolerances used are specified with the peak template command. All peaks that fall within the same cluster are linked together.
nv_peak compress ? LIST?: Compresses the peak list by permanently removing peaks that have been marked for deletion. After compression, deleted peaks cannot be restored! The peak list compressed is the active list if "LIST" argument is not specified, otherwise the specified list is examined.
nv_peak delete ? peakSpecifier ?: Deletes the specified peak. If no peak is specified the current peak of the active list is deleted. The peak can be restored with the peak undel command, or from the peak analysis window. The peak is permanently lost if the peak list is compressed. Peaks marked for deletion are not saved in the database when the database is written.
nv_peak delregion ? LIST?: Deletes the peaks in the peak list whose centers are in the active box. The peak list examined is the active list if "LIST" argument is not specified, otherwise the specified list is examined.
nv_peak display ? LIST?: Draw boxs and labels at the position of all the peaks in the peak list. The peak list displayed is the active list if "LIST" argument is not specified, otherwise the specified list is displayed. For example, peak -display noesy, would display all the peaks in the peak list named "noesy". Display occurs in the active window. The peak-display list can also be set in the PEAK_ATTRIBUTES_PANEL.
nv_peak dmatch ? listA listB?: Execute the peak double-matching algorithm to compare the two peak lists, listA and listB. Prior to using this command use the peak template command to set up the search template. Only peak fields specified in the template will be compared. The command creates two tcl array variables, dmA, dmB. There is one element in each array for each peak from the corresponding list. If the element is positive, it is the index of the peak in the other list that double-matches. If it is negative, it is the index of the peak in the other list that was closest, but the match was not a double match. A double match occurs if the following conditions are met: Consider two peaks Ai and Bj from two peak lists listA and listB. The distance between peaks Ai and Bj must be within the specified tolerances for each dimension (specified with the search template). The peaks double match, if and only if, Bj is the peak in list B that is closest to Ai, and Ai is the peak in list A that is closest to peak Bj. If a negative tolerance is specified in the search template, nv_peaks match only if the dimensions with the negative tolerance are not within the tolerance. This can be used, for example, when comparing two 4D lists and one wants to exclude matches where all 4 dimensions agree. This command also returns as its result a list of the dimension names and the corresponding rms deviation between pairs of double matched peaks in the two lists.
nv_peak element elemSpecifier peakSpecifier ? value ?: Returns the value of the element specified for the specified peak. If the optional argument is included the command sets the element to the value specified. The valid elements are: nv_peakLabel The chemical shift of along the specified dimension. nv_peakLabel.P The chemical shift of along the specified dimension. nv_peakLabel.W The peak width for the specified dimension. nv_peakLabel.L The atom label for the specified dimension. nv_peakLabel.E The peak error message for the specified dimension. int The peak intensity. vol The peak volume. For example, nv_peak elem 15N.W hnco.45 would return the peak width for the 15N dimension of peak 45 of the list hnco.
nv_peak find LIST ppm1 ppm2 ...: Returns a list of the numbers of the peaks in the specified peak list that are within a specified tolerance of the specified chemical shifts (ppm1, ppm2 ...). The tolerance and peak dimensions to test are specified with the peak template command, see below. If the character "-" is specified as the LIST argument, the active list is used.
nv_peak inbox ? LIST?: Returns a list of the numbers of the peaks from a peak list whose centers are within the cursor box. The peak list examined is the active list if "LIST" argument is not specified, otherwise the specified list is examined. For example, peak inbox hmqc, would find the peaks in the peak list named "hmqc" that are within the cursor box in the active window. The peaks in the list are sorted according to their distance from the center of the box.
nv_peak label ? LIST?: Returns the labels for the various dimensions of the peak list. The nv_peak list used is the active list if "LIST" argument is not specified, otherwise the specified list is used.
nv_peak link peakSpecifier1 ? peakSpecifier2 ?: If only one peak specifier is included, the command returns a list of nv_peaks that are linked to the specified peak. If two peakSpecifiers are included a link is created between the two peaks. The format of the peakSpecifier must include the link dimension as well as the list name/number and peak number. For example, noesy.35.0 would specifiy dimension 0 of peak 35 of list noesy.
nv_peak match LIST arg ...: Returns a list of peaks for which any of the peak labels match the arguments. For example, peak -match noesy 14.hn, would return any the peak specifiers for any peaks in the list named noesy that had a label of 14.hn for any of the dimensions. Wild cards can be used. For example, peak match * 33.c*, would return the peak specifiers for any peaks in any of the lists that had a carbon of residue 33 has the peak label. More than one argument can be used. For example, nv_peak -match noesy 14.ha 15.hn, would return any peaks of the list named "noesy" that had labels of 14.ha and 15.hn.
nv_peak mknoelist LIST nDim lab1 lab2 .. labnDim maxDis i0: Creates a new list named LIST with number of peak dimensions specified by nDim. The peak labels for each dimension are specified by the lab arguments. Entries are made for any pairs of protons that are less than maxDis apart. The intensity is calibrated with the isolated spin pair approximation using I=C*r^6. The constant C is calculated by assuming that a pair of protons with distance 2.0 E would have the intensity specified with the i0 argument. BUG: Not tested in new version.
nv_peak n ? LIST?: Returns the number of peaks (as a TCL result) in the peak list. The peak list counted is the active list if "LIST" argument is not specified, otherwise the specified list is counted.
nv_peak nearest ? LIST?: Returns a list of peaks close to the cursor. The peak list examined is the active list if "LIST" argument is not specified, otherwise the specified list is examined. Note: the peaks located will be closest to the cursor position, not the mouse position. For example, peak nearest noesy, would find the peaks in the peak list named "noesy", that are close to the cursor position. The list of peaks returned is sorted in order of the distance of the peaks from the cursor. Thus, the first peak in the list is the closest. If no peaks are within a certain tolerance, an error message will be returned.
nv_peak panel ? peakSpecifier?: Changes the peak analysis window to display information about the specified peak. The command also returns as its result the nv_peakSpecifier for the peak active in the peak analysis window.
nv_peak pick ? -box | -win ? ? -app | -new | -rep ?: ? -f1 -f2 -f3 -f4 ? peakListName Peak picks the active window using the modes specified by the optional arguments. -box Pick peaks in region bounded by crosshairs. -win Pick peaks anywhere in window. -app Append picked peaks to the list specified with peakListName. -rep Replace the list specified by peakListName with the newly picked peaks. -new Store picked peaks in a new list specified with peakListName. -f1, -f2, -f3, -f4 Allow peaks to wrap to other edge for the specified dimension BUG Check this command.
nv_peak put peakSpecifier ? tclVariable ?: NOT FUNCTIONAL Puts peak data into the peak specified with the peakSpecifier argument. The nv_peak data is taken from the variable named "PEAK", unless the optional tclVariable argument is included. If tclVariable is specified the data is taken from an arrayed variable named tclVariable.
nv_peak sf ?LIST sf1 sf2 ...?: Returns the spectrometer frequency for each dimension of the peak list. If the LIST argument is not specified then the current list for the active window is used. The spectrometer frequencies for a peak list are initially set to those of the spectrum that was initialy picked. If the optional sf1,sf2 ... arguments are included the spectrometer frequencies are changed to the specified values.
nv_peak status peakSpecifier ? peakStatus: Returns the status flag for the peak specified with the peakSpecifier argument. If the optional peakStatus argument is included the status flag of the specified peak is set to the specified value. Peaks with negative status values are marked for deletion. They do not appear when the list is displayed on a spectra and will be permanently removed when the list is compressed.
nv_peak sw ?LIST sw1 sw2 ...?: Returns the sweepwidth for each dimension of the peak list. If the LIST argument is not specified then the current list for the active window is used. The sweepwidths for a peak list are initially set to those of the spectrum that was initialy picked. If the optional sw1,sw2 ... arguments are included the sweepwidths are changed to the specified values.
nv_peak swap LIST label1 label2: Locates any peaks with labels label1 or label2 and exchanges the two labels. This command is useful for changing prochiral atoms. For example, nv_peak swap noesy 24.hb1 24.hb2 could be used to exhange the labels for the beta-methylene protons of residue 24 in the peak list named "noesy". If an asterisk, "*", is used for the LIST argument matching peaks from all the lists have their labels swapped.
nv_peak template LIST ? name ppm ... ?: Specifies a template to be used by the nv_peak find and peak dmatch commands, and returns the current template. For example, if the template is specificied as, nv_peak template hmqc 1HN 0.1 15N 0.3 then a peak find command like nv_peak find hmqc 8.3 118.2 would find all peaks whose 1HN chemical shift is within 0.1 ppm of 8.3 ppm, and whose 15N chemical shift is within 0.3 ppm of 118.2 ppm. The number of name:ppm pairs in the peak template command should match the number of ppms specified in the peak find command for each peak list used.
nv_peak undelete: Undeletes the specified peak. If no peak is specified the current nv_peak of the active list is restored. The peak is permanently lost if the peak list is compressed.
nv_peak undelregion ? LIST?: Undeletes the peaks in the peak list whose centers are in the active box. Note: Once peak the peaklist has been compressed the peaks can not be restored. The peak list examined is the active list if "LIST" argument is not specified, otherwise the specified list is examined.
nv_peak zlink LIST: All links of peaks from list LIST are zeroed.
nv_peak show ? peakSpecifier?: Drives the display of any spectral windows with the "ShowPeak" attribute set to "Expand", "ExpandFix", or "Plane" to show the appropriate region around the specified peak.
nv_peak unlink peakSpecifier: Removes any links between the specified peak and any other peak. BUG Check this
nv_peak list: Returns a list of the names of all peak lists in the database.
nv_peak name list ? newName ?: Returns the name of the specified list. If the optional argument newName is included it changes the list's name to the specified value.
nv_peak fold peakSpecifier up|down: Increments or decrements the chemical shift of the specified peak by an amount corresponding to one "sweep width". The peakSpecifier must include a dimension field. For example, "hnco.32.0".
nv_peak idtol listName ? idTol1 idTol2 ... ?: Returns or sets the tolerance used by the idpeak command. You must specifiy one value for each dimension of the list. For example, nv_peak idtol noesy 0.1 0.3 nv_peak idtol noesy3d 0.1 0.3 0.4
nv_peak pattern listName ? pattern1 pattern2 ... ?: Returns or sets the pattern used by the idpeak command (and potentially other commands as well). The pattern is in the form of an atomSpecifier, typically with the letters "i" or "j" replacing the residue field. For example: i.hn, j.ca Wild cards may be used: i.h* The residue field may include an integer offset: i-1.h* To set the pattern for an cbca(co)nnh experiment: nv_peak pattern cbcaconnh i-1.c* j.n j.hn This command needs to be extended to allow more complicated expressions.
nv_peak relation: Returns or sets the relation fields that specify the "familial" relation between peak dimensions. Dimensions that are the parent of other dimensions would be specified as P(1). Where the "1" is an integer specify the dimension that the specified field is the parent of. For example, an 1H,15N sqc experiment might have the relation: "" P(1), indicating that the atom of the second dimension (the nitrogen) is the parent of the atom of the first dimension (the proton).
nv_peak compare
nv_peak couple ? -ignore|-inphase|-anti ? -wDim min max: Couples together peaks that are within the specified tolerances. For example, nv_peak couple -inphase -w1 0 3 -w2 0 20 would couple together any peaks whose centers were between 0 and 3 Hz apart in the first dimension, and between 0 and 20 Hz apart in the second dimension, and whose intensities had the same sign.
nv_peak addlist listName label1 ? label2 label3 ... ?: Create a new list with the name 'listName'. The number of dimensions is determined by the number of 'label' arguments, and each of these arguments specifies the name of a dimension. For example, nv_peak addlist sqc 1HN 15N
nv_peak analyze datasetName -p1 plane -p2 plane peakSpecifiers ...: Analyze the region of the specified dataset contained within the bounds of the specified peaks. One or more peaks may be specified. If more than one peak is specified then the region is the smallest region that can encompass all the specified peak bounds. If the number of dimensions of the peak is less than the number of dimensions of the spectrum, then the additional plane specifiers are necessary. For example to evaluate the region of a 2D peak in a 3D spectrum, where each plane is a different relaxation time. nv_peak analyze T1exp -p1 7 t1exp.32 The command returns a list of values, for example, center 1.9946 jitter 1.9946 min 0.2489 max 1.9946 extreme 1.9946 volume 18.0795 mean 0.9040 sdev 0.5021 The values are also put into a Tcl array variable named Nv_Value, with indices "center", "jitter", "min" etc.