NMRVIEW COMMANDS

SUMMARY

This section lists, in alphabetical order all the NMRView specific commands. These can be executed by entering them on the command line or in tcl procedures. There are many other commands that are generic to tcl, and are described in the tcl manual. The NMRView commands are summarized below, with more detailed descriptions following the summary list. Some of the terms used in the command list are described in the GLOSSARY.

atom: Get or set data about individual atoms
calc: Calculate geometrical values from structures
cluster: Cluster a series of values.
contour: Contour plot active window.
create: Create a molecular structure and sends it to the viewer.
database: Read or write databases.
dataset: Interact with spectral datasets.
dcon: Interact with distance constraint list.
display: Specify atoms to be used when sending structures to the Molecular Data Viewer.
draw: Draw lines etc. in spectral window.
gencoord: Calculate Cartesian coordinates from internal coordinates.
getresidue: Get data about a specified residue.
getpkval: Get intensity data from spectrum in a region bounded by a peak box.
getval: Get intensity data from spectrum in a region specified by the crosshairs.
gridsrch: Grid search of conformational data.
idnoe: Identify unknown noes.
kpc: Calculate coupling constant with Kim-Prestegard method.
match: Specify atoms to be used when superimposing structures.
mdv: Interact with molecular data viewer.
noe: Interact with noe list.
peak: Interact with peak lists.
print: Get and set parameters dealing with the printer.
respan: Interact with residue display panel.
savg: Average coordinates.
select: Select structures for superposition and analysis.
sread: Read molecular structure files.
struct: Get data about structures.
super: Superimpose structures.
win: Interact with spectral windows.
write: Write molecular structures.
xy: XY plotting and fitting.

COMMAND DESCRIPTIONS

atom

Get or set data about individual atoms.

atom -num atomSpecifier

Returns the atom number of the specified atom. Atom specifiers are of the form residueNumber.atomName. For example 3.ca or 4.hn.

atom -elem elemName atomNum ? value ?

Returns the value of the element specified for the specified atom. If the optional argument is included the command sets the element to the value specified. The valid elements are:

ppm: The chemical shift of the specified atom.
x: The x coordinate of the specified atom.
y: The y coordinate of the specified atom.
z: The z coordinate of the specified atom.
parent: The atom number of the atom's parent.
seq: The sequence number of the specified atom.
rnum: The sequence number of the specified atom.
aname: The name of the specified atom.
rname: The residue name of the specified atom.

match ? atomSpecifier [on/off] ?

This command specifies what atoms are to be used when superimposing structuures. For example, to use backbone atoms use the following:

		match * off
		match *.ca on
		match *.c on
		match *.n on

calc ? arg ... ?

Calculate geometrical values from current structure. Valid options are as follows:

calc -disatom1 atom2: Calculate the distance between atom1 and atom2 and return the result.
calc -dih atom1 atom2 atom3 atom4: Calculate the angle between the plane containing atom1, atom2 and atom3, and the plane containng atom2, atom3 and atom4 and return the result.
calc -val atom1 atom2 atom3: Calculate the valance angle between atom1, atom2 and atom3 and return the result.
calc -vol atom1 atom2 atom3 atom4: Calculate the volume of the tetrahedron bounded by the four specified atoms.

cluster clustTol ? val1 val2 ... ?

Clusters a list of 2 or more values and returns a Tcl list containing the result. The clustering is done with a tolerance of clustTol. Each element of the returned list represents a cluster and is itself a list with the following elements: The average value of the elements in the cluster. The number of elements in the cluster. The indices of the values from the original list for the elements that fall in the particular cluster.

create -option molName

The create command creates a molecular structure and sends it to the Molecular Data Viewer with the name "molName". The atoms in the current NMRView structure that are used for display are those previously set for display with the "display" command. The bond connectivity between the atoms depends on the -option parameter.

create -molecule molName: Create a molecular structure for display and send it to the Molecular Data Viewer. Atom connectivity in the display will be according to the covalent bond connectivity of the current NMRView structure.
create -chain molName: Create a molecular structure for display and send it to the Molecular Data Viewer. Bonds will be drawn between sequentially adjacent atoms (that are set for display) in the current NMRView structure. For example, if only CA atoms are set for display, the bonds will be drawn from one CA atom to the next, resulting in a CA backbone trace.

database ? arg ?

The database command allows one to read and write the spectral database. DO NOT USE UNTIL FURTHER NOTICE. The database named "NMRView.gdbm" is automatically created.

database -read fileName: Read the database named fileName .
database -write ? fileName ?: Writes the current database to disk. The original database is saved as fileName.BAK.
database -close: Writes the current database to disk. The original database is saved as fileName.BAK.

dataset ? arg ?

The dataset command...

dataset -open fileName

Opens the dataset specified by fileName . You can open a group of files by using this command in combinatin with some Tcl commands. For example, to open all the files in a directory that end with ".nv" use:

foreach file [glob *.nv] {dataset -open $file}.

dataset -rdpar datasetName

Reads a parameter file associated with the dataset specified with datasetName.

dataset -wrpar datasetName

Writes a parameter file associated with the dataset specified with datasetName.

dataset -ref datasetName dim ? arg ?

Returns the chemical shift at the reference point for dimension dim of dataset datasetName. If the optional argument is specified the chemical shift is changed to the new value. For example, dataset -ref hncoca.mat 2 182.3, changes the chemical shift along dimension 2 of the dataset named hncoca.mat to 182.3.

dataset -refpt datasetName dim ? arg ?

Returns the datapoint at which the reference chemical shift is specified for dimension dim of dataset datasetName. If the optional argument is specified the data point used for reference is changed to the new value. For example, dataset -refpt hncoca.mat 3 17, changes the sweepwidth along dimension 3 of the dataset named hncoca.mat to 17.

dataset -sf datasetName dim ? arg ?

Returns the spectrometer frequency for dimension dim of dataset datasetName. If the optional argument is specified the spectrometer frequency is changed to the new value. For example, dataset -sf hncoca.mat 1 600.5, changes the spectrometer frequency corresponding to dimension 1 of the dataset named hncoca.mat to 600.5.

dataset -sw datasetName dim ? arg ?

Returns the sweepwidth set for dimension dim of dataset datasetName. If the optional argument is specified the sweepwidth is changed to the new value. For example, dataset -sw hncoca.mat 3 1800, changes the sweepwidth along dimension 3 of the dataset named hncoca.mat to 1800.

dcon -option ? arg ... ?

The dcon command is used to manipulate the distance constraint list by setting and retrieving parameters, as well as writing constraint lists for XPLOR and PEGASUS. The arguments used depend on the particular option, as described below. The dcon command can take any of the following forms:

dcon -clear: Clear the distance constraint list.
dcon -elem elemSpecifier iConstr ? value ? Returns the value of the the element specified with the elemSpecifier for the constraint specified with the iConstr argument. If the optional value argument is specified the comand sets the noe's element to that value. The valid elemSpecifiers:

noe
The noe this constraint is derived from.
low
The lower limit of this constraint.
up
The upper limit of this constraint.
pseudo
The pseudo atom correction that will be applied for this constraint.
res.0
The residue number of the first atom of this constraint.
res.1
The residue number of the second atom of this constraint.
aname.0
The atom name of the first atom of this constraint.
aname.1The atom name of the second atom of this constraint.
dcon -n: Returns the number of distance constraints in the list.
dcon -gen: Generates an internal (to NMRView) constraint list from the internal noe list. Constraints involving non-stereospecifically assigned protons are optimized in manner similar to that used in the program DIANA (Guntert et al., J. Mol. Biol. (1991) 217:517-530. At present, the constraint list is not saved in the database.
dcon -pegasus fileName: Create a constraint file named, fileName , in the format used by PEGASUS. Constraints will be taken from the constraint list.
dcon -xplor fileName: Create a constraint file named, fileName , in the format used by XPLOR. Constraints will be taken from the constraint list.

display ? atomSpecifier [on/off] ?

This command specifies what atoms are to be used when sending structu res to the Molecular Data Viewer. For example, to send only the coordinates of backbone atoms use the following:

                display * off
                display *.ca on
                display *.c on
                display *.n on

To send all atoms use:

		display * on

To send residues 5 to 20 use:

		display *  off
		display 5-20  on

draw ? arg ... ?

Draws lines or boxes in current spectral window.

draw -box x y xw yw: Draw a box center at with width wx,wy .
draw -color colorNum: Sets drawing color to colorNum .

gencoord: Calculate cartesian coordinates from internal coordinates. Only valid if a PEGASUS sequence has been read.

getresidue resNum ? varName ?

Returns data about the residue specified with resNumber . Data is returned in a arrayed tcl variable named varName . The elements of the array are

natoms: The number of atoms in the residue.
first: The atom number of the first atom in the residue.
last: The atom number of the last atom in the residue.
name: The name of the residue (Phe, Asp, Tyr ... )
atomName: For each atom in the residue there is an array element whose index is the name of the atom. The value is the atom number of that atom.

getpkval -? valType ? datasetName peakSpecifier: Gets intensity data from the dataset specified in datasetName. The dataset must be opened (with Datasets Add) though it need not be displayed in a window. The region used is that contained within the box bounded by the peak specified by the peakSpecifier (peakList.peakNumber). The type of data calculated is dependent on the valType argument and is the same as that used with the getval command.

getval -? valType ?

Gets intensity data from cursor region of active window. The cursor region is a box, centered on crosshair 1, and bounded in one corner by crosshair 2. It is not the region between the two crosshairs. The type of data calculated is dependent on the valType argmuent as follows:

-vol: Return the sum of the points in the cursor region.
-max: Return the maximum value from the cursor region.
-min: Return the minimum value from the curror region.
-ext: Return the most extreme (maximum or minimum) value from the cursor region.
-mean: Return the average value in the cursor region.
-center: Return the value at the center of the cursor region.
-sdev: Return the standard deviation of the values in the curror region.
-all: Return all of the above values in an arrayed Tcl variable named VALUE. The array has elements VOLUME, MIN, MAX, EXTREME, SDEV, MEAN, and CENTER. If the optional argument valType is not included, the value at the center of the cursor region is returned. The cursor region is defined as the rectangle centered on crosshair 1, and bounded at one corner by crosshair 2.

gridsrch -option

Read a grid file and do a search of grid search to find dihedral angles where the conformation is consistent with specified couplings and noes.

gridsrch -rea fileName: Read a grid file named fileName.
gridsrch -sea lower upper relativeValues relativeVariables: Execute the gridsearch.

idnoe ? -option arg ...?

The idnoe command is used to identify to identify the various atoms that could give rise to a particular cross peak.

idnoe ? arg ...?: Return the identity of protons that match the chemical shifts specified with the arguments. For example, idnoe 3.0 4.0, would return a list of pairs of protons, one of which is within a specified tolerance of 3.0 ppm, and the other of which is within the specified tolerance of 4.0 ppm. An additional constraint can be specified so that the protons have to match not only the specified chemical shift, but must be the bonded to an atom of the specified type at the specified chemical shift. For example, idnoe 3.0(C*@54.0) 4.0, would return only protons within the specified tolerance of 3.0 ppm that are bonded to a carbon (of any type, note the wildcard) within the specified tolerance of 54.0 ppm, and any protons within the tolerance of 4.0 ppm. idnoe 3.0(CA*54.0) 8.0(N@117.0), would return only protons within the specified tolerance of 3.0 ppm that are bonded to an alpha carbon at 54.0 ppm, and protons within a specified tolerance of 8.0 ppm bonded to a nitrogen at 117.0 ppm. The tolerance is specified by following the chemical shift value with ~tolValue. For example, idnoe 3.0~0.05 6.0~0.1. The tolerance need only be specified the first time the command is used, as it is remembered for subsequent instances.
idnoe -s: Sort the chemical shift data base. This command should be issued after any changes are made in the chemical shift assignments and prior to using the idnoe command.

kpc absSplit disSplit: Use the Kim-Prestegard method to calculate a coupling constant corrected for linewidth effects. The arguments specify the splitting between the absorbtion mode and dispersive mode peaks. The calculated coupling constant is returned.

mdv ? arg ... ?: The mdv command, without any arguments initializes the Molecular Data Viewer. The command, mdv exit, will stop the Molecular Data Viewer. Any other arguments are sent to the Molecular Data Viewer and interpreted by it. See section on the Molecular Data Viewer for the MDV commands.

noe -option ? arg ... ?

The noe command is used to manipulate the noe list by setting and retrieving parameters, as well as generateing constraint lists for XPLOR and PEGASUS. The arguments used depend on the particular option, as described below. The noe command can take any of the following forms:

noe -extract peakList ? scaleVal ?: Search the specified peakList for entries that have two named protons. For each such peak enter an noe into the noe list. If the optional argument scaleVal is specified, set the scale value for that NOE to the specified value.
noe -check: Inactivate noes that are between protons that have a fixed distance, or where the maximum distance is less than the upper bound.
noe -clear: Clear the noe list.
noe -n: Returns the number of noes in the noe list.
noe -uniq: Inactivate duplicate noes. In the current version of the software the most intense peak is retained.
noe -elem elemSpecifier iNoe ? value ? Returns the value of the the element specified with the elemSpecifier for the NOE specified with the iNOE argument. If the optional value argument is specified the comand sets the noe's element to that value. The valid elemSpecifiers:

int
The peak intensity of the peak this noe came from.
vol
The peak volume of the peak this noe came from.
scale
The scale value for this noe.
low
The lower bound for this noe.
upper
The upper bound for this noe.
pseudo
The pseudoatom correction appropriate for this noe.
list
The peaklist number that this noe came from.
number
The peak number that this noe came from.
stereo.0
The stereo specificity of the first atom of this noe.
stereo.1
The stereo specificity of the second atom of this noe.
res.0
The residue number of the first atom of this noe.
res.1
The residue number of the second atom of this noe.
aname.0
The atom name of the first atom of this noe.
aname.1The atom name of the second atom of this noe.
pname.0
The atom name of the first atom of this noe, with wild carding for the stereo specificity.
pname.1
The atom name of the second atom of this noe, with wild carding for the stereo specificity.
active
Set to "1" if noe will be used to generate a constraint. Set to "0" if noe will not be used to generate a constraint.

peak ? args ... ?

Various peak things.

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 peak to zero.

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.

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.

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.

peak -del ? 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.

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.

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.

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, 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.

peak -elem 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:

peakLabel: The chemical shift of along the specified dimension.
peakLabel.W: The peak width for the specified dimension. peakLabel.L; The atom label for the specified dimension.
peakLabel.E: The peak error message for the specified dimension.
int: The peak intensity.
vol: The peak volume.

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.

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.

peak -label ? LIST?

Returns the labels for the various dimensions of the peak list. The peak list used is the active list if "LIST" argument is not specified, otherwise the specified list is used.

peak -link peakSpecifier1 ? peakSpecifier2 ? If only one peak specifier is included, the command returns a list of 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.

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, 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.

peak -mknoe 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.

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.

peak -near ? 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 -near 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.

peak -pan ? peakSpecifier?

Changes the peak analysis window to display information about the specified peak. The command also returns as its result the peakSpecifier for the peak active in the peak analysis window.

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

peak -put peakSpecifier ? tclVariable ?

NOT FUNCTIONAL Puts peak data into the peak specified with the peakSpecifier argument. The 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.

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.

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.

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.

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,

peak -swap noesy 24.hb1 24.hb2

could be used to exhange the labels for the -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.

peak -template LIST ? name ppm ... ?

Specifies a template to be used by the peak -find and peak -dmatch commands, and returns the current template. For example, if the template is specificied as,

peak -template hmqc 1HN 0.1 15N 0.3

then a peak find command like 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.

peak -undel

Undeletes the specified peak. If no peak is specified the current peak of the active list is restored. The peak is permanently lost if the peak list is compressed.

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.

peak -zlink LIST

All links of peaks from list LIST are zeroed.

print args...

The print command provides an interface to various parameters that control printing of spectral plots.

print -autoprint ? arg ?: Returns the value of the autoprint command. If set to true, the print file is automatically sent to the printer. If the optional argument is specified the autoprint paramter is set to the specified boolean value.
print -file ? fileName ?: Returns the name of the file that the postscript data will be stored in when doing creating a hardcopy of spectra. If the optional argument is specified the filename is set to the specified value.
print -mode ? arg ?: Returns the printmode as landscape or portrait. If the optional argument is specified the printmode is set to the specified value.
print -printer ? arg ?: Returns the name of the printer that the plot file will be sent to if the autoprint parameter is set to true. If the optional argument is specified the printer name is set to the specified value.
print -size ? x y ?: Returns the size of paper that will be used.

sread -option fileName ? arg ?

Reads in one or more files, the type of which is specified by the option.

sread -pdb fileName: Read Protein Data Bank format files. This is the standard way to read in pdb files. NMRView first reads the pdb file to determine the amino acid sequence. Next, it reads the corresponding residues from the PEGASUS residue library. Finally, it reads coordinates from the pdb file for those atoms that have names matching the names in the residue library. Atoms, that do not have a match in the residue library will not be entered into the PEGASUS structure list. Atoms that are in the residue library but not in pdb file, will be included in structure list but will not be displayed. The file will be read from directory $SDIR where SDIR is a TCL variable. SDIR can be set in the preference panel or on the command line. The default value for SDIR is ".".
sread -grp fileName: Reads in coordinates from a series of PDB files. The first file is "filename0", second file is "filename1" etc. The command continues to read files until a file is unsuccesfully read or the maximum of 100 files have been read in. Each coordinate set is stored in successive structures. The command only reads in the coordinates. The commands "sread -seq", "sread -xpsf" or "sread -pdb" must have been used previously with a file with the same atoms. The directory used is the same as that used with "read -pdb" command.
sread -pdbs fileName: Read protein data bank files. Reads a file of atomic coordinates of a macromolecule. File must be stored in the PDB format as defined by Brookhaven National Laboratorie Protein Data Bank. This command does not also read from the PEGASUS residue library so no connectivity information is available. If this is needed use the pdb command instead. The directory used is the same as that used with "sread -pdb" command.
sread -mol fileName: Read MOLedit format files Reads in structure from file "filename" in MOLEDIT format. The directory used is the same as that used with "sread -pdb" command.
sread -xpsf fileName: Reads a file in the format produced by XPLOR. This is a alternative method to the sread -seq command to obtain atom, residue and connectivity information. Coordinates must be read in with the "sread -xyz" or "sread -grp" commands. The directory used is the same as that used with "sread -pdb" command.
-xyz fileName strct: Reads the PDB file filename and attempts to match the atoms to atoms in the structure in memory. If atoms match by residue name, atom name, sequence number, chain id, and alternate identifier then the coordinates corresponding to each atom matched are assigned the value of the coordinates of that atom in file. The coordinates are read into the structure specified by the "strct" parameter. The directory used is the same as that used with "sread -pdb" command.
-seq seqName: Read in residues from residue library based on sequence in file filename.

respan -option ? arg ... ?

This command provides an interface to the sequential assignment panel.

respan -seq: Returns the sequence number of the residue currently displayed in the sequential assignment panel.
respan -atom: Returns a list of all the atom names that are currently selected in the sequential assignment panel.
respan -menu ? tclProc args ... ?: Adds an entry to the user menu of the sequential assignment panel. When the menu entry is selected a tcl procedure named tclProc will be executed with the associated arguments.

savg ? structure ?: Create a new set of coordinates that are the average of the coordinates of all selected coordinates. The resulting structure will be stored in the structure number one greater than the last current structure. For example, if there are 8 structures (0.. 7) currently in memory the average structure will be stored in structure 8. If the optional argument is specified the structure will be stored in the specified structure location.

select args ...

NMRVIEW can store internally up to 100 coordinate sets (structures) corresponding to an individual sequence. The command select allows the user to include or exclude specific structures from display and superpositioning. The default state is for all structures to be included. The first structure is number 0. to the structures to be used for display and superpositioning. The wildcard "*" can be used to add all structures. from those structures used for display and superpositioning. The wildcard "*" can be used to exclude all structures.

select - * + 3: Use only structure 3 for display.
select - 5: Exclude structure 5 from display and superpositioning.
select - * + 2 3 8: Use only structures 2, 3 and 8 for display and superpositioning.

super ? -f fixStructure -m movStructure ?: The super command calculates rms deviations between coordinates of currently stored structures. A matrix of rms values between all pairs of selected structures is reported. Only structures selected with "select" command, and atoms select with "match " command are used in the comparison. Without any options super does not actually change the coordinates of the structures. With the -f option, the structures are moved so as to minimize the rms deviation with the structure specified with the fixStructure parameter. By default, all structures are moved. The -m option can be used to restrict the command so that only the structure specified with the movStructure parameter is moved. For example, "super -f 1 -m 2" will superimpose structure 2 on structure 1."super -f 2" will superimpose all selected structures on structure 2.

win-optionargs ...The win command is used to set and retrieve parameters related to the spectral display windows. The arguments used depend on the particular option, as described below. When used to retrieve parameters the desired parameter is return as a TCL result and can be used in a "set" command. Commands returning two or more parameters, for example ``win -x``, return the result as a TCL list. The win command can take any of the following forms:

win -aclear ? clearMode?

Returns the autoclear mode of the active window. If the optional argument is specified the autoclear mode is set for the window is set. If clearMode is 1, the autoclear mode is set to TRUE and the window will be cleared each time a spectrum is drawn. If clearMode is 0 the autoclear mode is set to FALSE, and subsequent spectra will overlay the current spectra.

win -act ? winName?

Returns the name of the active window. If the optional argument is specified the active window is set to the window named winName. For example, win -act b sets window "b" to be the active window.

win -attributes

Display Attributes window.

win -clm ? contourLevelMultiplier?

Returns the contour level multiplier used in the active window. If the optional argument is specified the contour level multiplier in the active window is set to contourLevelMultiplier. For example, win -clm 1.5, sets the contour level multiplier in active window to 1.5.

win -clear ? all?

Clears the active window. If the all argument is included all the entire X-window is cleared including all daughter windows.

win -copy

Copy data about active window into a buffer.

win -cre winName ? wx wy x y ?

Creates a new window for spectral display. The winName argument specifies the name of the new window. Optional arguments specify the size (wx and wy) and position (x and y) of the new window. For example the command win -cre a 700 500 will create a window named "a" that has a size of 700 pixels wide by 500

win -cross1 ? x y?

Returns the coordinates (in ppm) of CrossHair_1 in the active window. If the optional arguments are specified the position of CrossHair_1 is set to x, y. For example, win -cross1 3.2 4.3, sets CrossHair_1 in the active window to (3.2,4.3) in ppms.

win -cross1x ? x?

Returns the x coordinate (in ppm) of CrossHair_1 in the active window. If the optional argument are specified the x value of CrossHair_1 is set to x. For example, win -cross1x 3.2, sets x value of CrossHair_1 in the active window to 3.2 in ppms. The y value is unchanged.

win -cross1y ? y?

Returns the y coordinate (in ppm) of CrossHair_1 in the active window. If the optional argument are specified the y value of CrossHair_1 is set to y. For example, win -cross1x 3.2, sets y value of CrossHair_1 in the active window to 3.2 in ppms. The x value is unchanged.

win -cross2 ? x y?

Returns the coordinates (in ppm) of CrossHair_2 in the active window. If the optional arguments are specified the position of CrossHair_1 is set to x, y. For example, win -cross2 3.2 4.3, sets CrossHair_2 in the active window to (3.2,4.3) in ppms.

win -cross2x ? x?

Returns the x coordinate (in ppm) of CrossHair_2 in the active window. If the optional argument are specified the x value of CrossHair_2 is set to x. For example, win -cross2x 3.2, sets x value of CrossHair_2 in the active window to 3.2 in ppms. The y value is unchanged.

win -cross2y ? y?

Returns the y coordinate (in ppm) of CrossHair_2 in the active window. If the optional argument are specified the y value of CrossHair_2 is set to y. For example, win -cross2x 3.2, sets y value of CrossHair_2 in the active window to 3.2 in ppms. The x value is unchanged.

win -dau

Create a daughter window in the active window. Daughter windows act like regular windows but are contained within the same frame as the parent. The first daughter window will be named parName.0, where parName is the name of the parent. For example, if the active window is named a, win -dau will create a daughter window named a.0. Subsequent daughter windows would be named a.1, a.2 etc. After createing the window, use the win -wx and win -wy commands to adjust the parent and daughter window to occupy non-overlapping space. See the tcl macro "splitwin.tcl" for an example. There is limit to the number of daughter windows that can be created in a single parent window.

win -dataset ? datasetName?

Returns the name of the dataset used in the active window. If the optional argument is specified the dataset for the active window is set to datasetName. For example, win -dataset noesy.mat, sets the dataset for the active window to "noesy.mat". The specified dataset must have been opened previously.

win -del

Delete the active window.

win -dim ? displayDimType?

Returns the display type as 0 (1Dx), 1 (1Dy) or 2 (2D). If the optional displayDimType argument the display type is set as specified.

win -dispeaks ? peakListName?

Returns the name of the peak list to be displayed in the active window. If the optional argument is specified the display peak list for the active window is set to peakListName. For example, win -dispeaks list1, sets the peak list for the active window to "list1". Whenever this window is redrawn the peaks from the specified list will be displayed. To cancel peak display for the window use the "peak -dispeaks none". See also the PEAK ATTRIBUTES PANEL.

win -draw

Draws the current window.

win -expand

Draws expansion (area in cursor box) of active peak.

win -full

Draws full expansion of active window.

win -grid

The grid command is a toggle command. If grids are off in the active window it causes a grid of points to be drawn in the active spectral window. The grid of points will be drawn each time the window is redrawn. If grids are currently on in the active window the grid command sets the window so the grid is not drawn when the window is redrawn. Each point in the grid is located at the position of a point in the file.

win -jmode ? jmodType?

Returns the method for displaying peaks that have J-values (coupling constants) greater than 0.0. With jmodType 0, a single peak is displayed with the J-value added to the peak width. With jmodType 1, two peaks are displayed with their centers shifted by the J-value.

win -lvl ? Level?

Returns the contour level of the active window. If the optional argument is specified the contour level of the active window is set to Level. For example, win -lvl 0.2 sets the contour level in active window to 0.2.

win -menu menuItem ? entryNum?

Adds an entry to the user pullright menu of the active spectral window. If the optional entryNum parameter is included the specified meu entry is changed to the new value. If the entry number is than the current number of entries, the new item is added after the last item. For example, win -menu "peak -delregion" 2 adds replaces item 2 in the list of user menu entries. The first menu entry is number 0.

win -mouse mouseKey mouseAction procName

This simple but powerful command provides the user with an extensive ability to customize the operation of NMRView. Experimentation with this command will be well worth the effort. This command specifies that the procedure named procName is to be executed when the mouse key specified my mouseKey undergoes theaction specified by the mouseAction argument occurs. The possible mouse actions are up, down, drag and double (for double click). Actions can be specified for the left and middle mouse keys. For example, after the command win -mouse left up show_a_peak has been executed, whenever the left mouse button goes up in the active window the command "show_a_peak x y", where "x" and "y" are the current mouse (not cursor) positions (in ppm), will be sent to the tcl command interpreter.

win -nwin

Return the number of spectral windows currently open.

win -negcolor ? colorName?

Returns the number corresponding to the color used for negative contours in the active window. If the optional argument is specified the color for negative contours in the active window is set to colorName. For example, win -negcolor 3 sets the color for negative contours in the active window to 3.

win -iwin winNum

Make the specified window (by window number) the active window. The window number runs from 0 to nwin-1 where nwin is the number of spectral windows (obtained with win -nwin). Windows are numbered sequentially in the order in which they were created.

win -nlvl ? nLevels?

Returns the number of contour levels used in the active window. If the optional argument is specified the number of contour levels in the active window is set to nLevels. For example, win -nlvl 5, sets the number of contour levels in active window to 5.

win -paste

Paste data from the copy buffer into active window and draw contour plot.

win -peak_col_off ? colorName ?

Returns the number of the color used to draw peak boxes that are not on (or between, if a range of planes is used) the displayed plane. If the optional argument is specified the number of color is set to that value in the active window. See also the PEAK ATTRIBUTES PANEL.

win -peak_col_on ? colorName ?

Returns the number of the color used to draw peak boxes that are on (or between, if a range of planes is used) the displayed plane. If the optional argument is specified the value is set in the active window. See also the PEAK ATTRIBUTES PANEL.

win -peak_col_type ? arg ?

If set to the value 0, peak boxes are colored according to their closeness to the display plane, as determined by the peak_off, peak_col_off, and peak_col_on parameters. If set to the value 1, peak boxes are colored according to the peak labels. If any peak dimension has a "?", in the label field the peak boxes is colored as specified by the peak_col_off argument, otherwise it is colored as specified with the peak_col_on. See also the PEAK ATTRIBUTES PANEL.

win -peak_dis_type ? arg ?

Returns a number (0/1) corresponding to the manner in which peaks from the peak list are displayed in the spectral window. If set to 0, peaks are drawn as boxes with widths corresponding to the peak width. If the value is 1, peaks are drawn as simulated contours. The peak width parameter is then assumed to be the line width. The number of contours and their levels are determined by the win -nlvl, win -lvl, and win -clm commands. If the optional argument is specified the value is set in the active window. See also the PEAK ATTRIBUTES PANEL.

win -peak_off ? nPlanes ?

This parameter determines which peaks are displayed on 3 or 4 dimensional spectra. If the plane of a peak is closest to the display plane, it is displayed with the color specified by the peak_col_on parameter. If it is not on the display plane, but is within nPlanes of the display plane it is displayed with the color specified by the peak_col_off paramter. Otherwise it is not displayed. See also the PEAK ATTRIBUTES PANEL.

win -peak_lab_type ? labType ?

This parameter determines what type of label is drawn next to each peak box. The choices are as follows:

0: The peak number.
1: The peak labels (for all peak dimensions).
2: The residue number of the peak (for all peak dimensions that have unique values.
3: The atom names of the peak (for all peak dimensions).

win -peakp Displays the peakpick panel.

win -plot ? all?

Make hardcopy plot of contour plot of active region. If the all argument is included all daughter windows of the current plot are plotted as well.

win -posi ? x y ?

Returns the position of the current window. If the optional arguments are specified the position of the active window is set to screen coordinates x,y. Note, the upper left corner of the screen is at 0,0. For example, win -pos 200 100 sets the active window position to (200,100). BUG NOTE. Does not return the position, but will set it.

win -poscolor ? colorName?

Returns the number corresponding to the color used for positive contours in the active window. If the optional argument is specified the color for positive contours in the active window is set to colorName. For example, win -poscolor 3 sets the color for positive contours in the active window to 3.

win -previous

Draw previous expansion (up to 8 previous expansion sare stored.)

win -search

Search for peaks (local maxima) perpendicular to plane at cursor position in the 3D spect rum in active window. This is good for finding what plane a peak is actually in when multiple planes have been displayed in spectral window.

win -showpeaks

Draw boxes in active window at positions of peaks in the active peak list.

win -siz ? x y?

Returns the size of the current window. If the optional arguments x and y are specified the size of the active window is set to x pixels wide by y pixels high. For example, win -siz 300 400 will change the active window size to 300 by 400 pixels. BUG NOTE: Does not return the size, but will set it.

win -swap

Swap x and y contour limits and redraw contour plot.

win -wx ? xMin xMax?

Returns the x limits of the area of the active window that is used to draw spectra in. If the optional arguments are specified the x limits of the area range from xMin to xMax. Limits are returned and specified as fractions of the window. For example, win -wx 0 0.5 sets the plotting area of the active window to the left half of the window.

win -wy ? yMin yMax?

Returns the y limits of the area of the active window that is used to draw spectra in. If the optional arguments are specified the y limits of the area range from yMin to yMax. Limits are returned and specified as fractions of the window. For example, win -wy 0 0.5 sets the plotting area of the active window to the top one-third.

win -xdim dimNum

Sets the x display dimension of the active window to dimNum.

win -x ? firstColumn lastColumn?

Returns the plot limits on the x axis in the active window. If the firstColumn and lastColumn arguments are specified the plot limits for the axis in the active window are set to firstColumn and lastColumn. If the argment is a number it is interpreted as a chemical shift in ppm. If the argument is a number followd by a "p", it is interpreted as a column number in points. For example, win -x 100p 6.3 sets the first column to point 100 and the last column to the point closest to 6.3 ppm.

win -xaxis ? bottomAxis topAxis?

Returns a 0 or 1 specifying whether or not the bottom and top axis labels and tick marks should be drawn. If the bottomAxis and topAxis arguments are specified the respective axes are turned on are off as specified. The values are specified as boolean values (0/1, yes/no, on/off or true/false).

win -xbor ? leftBorder rightBorder?

Returns the borders for the left and right sides of the plot region in the active window. If the leftBorder and rightBorder arguments are specified the left and right borders are set to the specified values. The values are specified in units of pixels.

win -y ? firstRow lastRow?

Returns the plot limits on the x axis in the active window. If the firstRow and lastRow arguments are specified the plot limits for the axis in the active window are set to firstRow and lastRow. If the argment is a number it is interpreted as a chemical shift in ppm. If the argument is a number followd by a "p", it is interpreted as a Row number in points. For example, win -x 100p 6.3 sets the first row to point 100 and the last row to the point closest to 6.3 ppm.

win -yaxis ? leftAxis rightAxis?

Returns a 0 or 1 specifying whether or not the left and right axis labels and tick marks should be drawn. If the leftAxis and rightAxis arguments are specified the respective axes are turned on are off as specified. The values are specified as boolean values (0/1, yes/no, on/off or true/false).

win -ybor ? bottomBorder topBorder?

Returns the borders for the bottom and top of the plot region in the active window. If the bottomBorder and topBorder arguments are specified the bottom and top borders are set to the specified values. The values are specified in units of pixels.

win -ydim dimNum

Sets the y display dimension of the active window to dimNum.

win -z ? firstPlane lastPlane?

Returns the first and last planes to be drawn in the active window for dimension z. If the firstPlane argument is specified, the first and last planes are both set to firstPlane. Thus only the specified plane will be drawn. If both the firstPlane and lastPlane arguments are specifed the the first plane will be set to firstPlane and the last z plane to lastPlane. When contour plot is performed all planes form the first to last, inclusive, will be drawn. If the argment is a number it is interpreted as a chemical shift in ppm. If the argument is a number followd by a "p", it is interpreted as a plane number. For example, win -z 5p 50.3 sets the first plane to plane 5 and the last plane to the plane closest to 50.3 ppm.

win -zdim dimNum

Sets the zdisplay dimension of the active window to dimNum.

win -z2 ? firstPlane lastPlane?

Returns the first and last planes to be drawn in the active window for dimension z2 (the fourth dimension). If the firstPlane argument is specified, the first and last planes are both set to firstPlane. Thus only the specified plane will be drawn. If both the firstPlane and lastPlane arguments are specifed the the first plane will be set to firstPlane and the last z plane to lastPlane. When contour plot is performed all planes form the first to last, inclusive, will be drawn. If the argment is a number it is interpreted as a chemical shift in ppm. If the argument is a number followd by a "p", it is interpreted as a plane number. For example, win -z 5p 50.3 sets the first plane to plane 5 and the last plane to the plane closest to 50.3 ppm.

win -z2dim dimNum

Sets the x display dimension of the active window to dimNum.

xy ? arg ... ?

This command blah blah.

xy -clear

Clear the xy display.

xy -clv? confLevel ?

Returns the confidence levels used in estimating the confidence intervals during a non-linear fit to the data. If the optional argument is specified the confidence level is set to confLevel. The default value is 0.9.

xy -col colorName

Sets the color used in drawing xy data.

xy -dump

Outputs the xy data to the console window.

xy -n? N ?

Returns the number of valid data points for plotting on the xy graph. If the optional argument is specified the number of valid data points is set to N.

xy -nsim? N ?

Returns the number simulations performed in estimating the confidence intervals during a non-linear fit to the data. If the optional argument is specified the number of simulations is set to N.

xy -nmax ? nMax ?

Returns the number of maximum number of data points that can be used for plotting on the xy graph. If the optional argument is specified the maximum number of data points is set to nMax. The default is 200.

xy -seed ? seedVal ?

Returns the seed value for random number generator. If the optional argument is specified the seed for the random number generatorthe is set to seedVal.

xy -xmin ? xMin ?

Returns the minimum value for the x axis. If the optional argument is specified the minimum value for the x axis is set to xMin.

xy -xmax ? xMax ?

Returns the maximum value for the x axis. If the optional argument is specified the maximum value for the x axis is set to xMax.

xy -ymin ? yMin ?

Returns the minimum value for the y axis. If the optional argument is specified the minimum value for the y axis is set to yMin.

xy -ymax ? yMax ?

Returns the minimum value for the y axis. If the optional argument is specified the minimum value for the y axis is set to yMax.

xy -x i ? xVal ?

Returns the x value for datapoint i . If the optional argument is included then set the x value for datapoint i to the specified value.

xy -y i ? yVal ?

Returns the y value for datapoint i . If the optional argument is included then set the y value for datapoint i to the specified value.

xy -s i ? sdVal ?

Returns the standard deviation value for datapoint i . If the optional argument is included then set the standard deviation value for datapoint i is set to the specified value.

xy -fit ? arg ... ?

Fit the xy data to the selected equation.

xy -eqn ? arg ?

Set the equation to be used in the non-linear fit to equation number arg

xy -display

Draw the xy data.

xy -gen ? param1 param2 ... ?

Generate simulated data using the parameters specified with param1 param2 ... .

xy -noise noiseValue

Add noise with a rms value of noiseValue to the Y value of the xy data.

xy -pkfit datasetName peakSpecifier1 ? peakSpecifier2 ... ?

Does a non-linear fit to optimize the fit of the one or more specified peaks to the data in the dataset specified by datasetName

xy -pkextr datasetName peakSpecifier1 ? peakSpecifier2 ... ?

Extracts the datapoints from the smallest region of the spectrum that encompasses all the peaks specified in the list of one or more specified peaks. The data is extracted from the dataset specified by datasetName

xy -rngextr datasetName ? -d1 x1 x2 ? ? -d2 y1 y2 ? ? -d3 z1 z2 ? ? -d3 z21 z22 ?

Extracts the datapoints from the specified region of the spectrum. If the limits for a specified dimension are not included, then the range of all points for that dimension are extracted. If the range specifiers are followed by a p (for example, 113p) the range is specified in data points, otherwise it is assummed to be in ppm. If only one of the two values for a given range is specified, then the two are assummed to be equal. The data is extracted from the dataset specified by datasetName Examples,

xy -rngextr -d1 0.3 1.2 -d2 7.0

xy -rngextr -d1 80p -d2 7.0 8.0

xy -rngextr -d1 1.2

write ? args ... ?

Write structures to files.

write -pdb ? -str structNum -select -sfile ? fileName: Write the current structure out in the format of a protein data bank (PDB) file. The file will be created with the name specified with the fileName argument. If multiple structures are present in memory the default action is to write all structures out to individual files. The files will be named, fileName0, fileName1 etc. The -str flag can be included to specify which structure is to be wrtten. In this case only the structure specified by the structNum argument will be written. For example, write -pdb -str 8 crambin, would write out structure number 8 (0 is the first structure) to a file named crambin.pdb. If the -select flag is specified, then only atoms that are currently selected (see the match command) will be included in the output file(s). If the -sfile flag is included all the structures will be concatenated into a single output file.