USEFUL COMMANDS AND PARAMETERS



USEFUL COMMANDS AND PARAMETERS, Nov. 1995 edition

|acqi |3 |“acquisition” This command brings up the acquisition window used to lock and shim samples. |

|aph |17 |“auto phase” This command carries out an automatic phasing. May fail when you have a low signal to noise ratio. |

|aph0 |17 |“auto phase the zero order term” This command autophases the frequency independent term, rp, only. |

|apt |19 |“attached proton test” This command sets up the spectrometer to do an attached proton test. (Used to indicate which carbons have even and which have odd numbers of attached |

| | |hydrogens). |

|aptaph |19 |“attached proton tests auto phase” This command auto phases apt data. |

|array |21 |“array” This parameter is used to set up a sequence of experiments where some variable is systematically incremented. |

|at |23 |“acquisition time” This parameter sets the length of time you collect the FID. The signal is strongest at the very start of the FID and rapidly drops off in intensity until it is |

| | |lost in the background noise, therefore you get the best signal to noise ratio by using the early part of the FID. The longer the FID you collect the better the digital resolution |

| | |you will get in the final spectrum (i.e., resolution is proportional to one over the at). However, after a certain acquisition time the signal is down to zero and all you are |

| | |collecting is noise. Therefore, short acquisition times give the best signal to noise ratio but poor resolutions while long acquisition times give poor signal to noise ratios but |

| | |excellent resolution: a classic trade off. Setting “at” at values just slightly longer than the end of the FID signal gives a good compromise for signal to noise and resolution, |

| | |while minimizing total data collection time. This is especially important for long data collections. Note: as “at” increases the “np” (number of points) increases as well. |

| | |Example: at = 3.75 sets the acquisition time at 3.75 seconds. |

|atex |23 |“append text” This command adds a line of text to the file. Example atext (‘bug eyes’) would print bug eyes on the data file. |

|au |24 |“automatic acquisition and processing” This command is like ga but also checks shims, lock, etc. for 1-D and 2-D equipment. |

|autodept |26 |“automatic dept” This command automatically processes dept data. |

|axis |31 |“axis” This command defines the identify of the axis. Example” axis = ‘h’ and axis = ‘p’ sets the axis in Hz and ppm, respectively. |

|bc |34 |“baseline correct” This command corrects the baseline. Examples: bc and bc(3) does 1st and 3rd order baseline corrections, respectively. |

|bs |37 |“block size” This parameter gives the number of transients to be collected before each set of data is written to disk in a long data collection. Its value is such that if you are on|

| | |a overnight acquisition set for 30,000 transient (i.e., nt = 30,000) and it crashes at 29,999 with bs = n then you lose all the data. If bs is too small you waste some collection |

| | |time and if it is too large a crash will cost more data. In practice though, its exact value is not critical and values of 16 or 64 are probably the most commonly used (use values of|

| | |2n). Example: bs = 16 sets the number of transients in each block as 16. |

|btune |37 |“broadband tune” This command sets the spectrometer to pulsing at the frequency of the observe nucleus in the current experiment. This command is used so that you can minimize the |

| | |feedback for that nucleus (i.e., tune the probe). This command should be done after the cables are moved to the tune meter and the quarter wavelength cables are changed (if |

| | |required). “tuneoff” cancels “btune”. |

|capt |40 |“carbon and APT” This command prepares parameters for a 13C followed by an APT spectrum. Example: capt (‘dmso’) nt = 1,000 au would automatically collect 1,000 scans of 13C and APT|

| | |and would be processed, in turn, by rttmp(‘C13’) and rttmp(‘apt’). |

|cdc |41 |“cancel drift correction” This command cancels the dc. |

|cdept |42 |“carbon and dept” This command prepares parameters for a 13C followed by a dept. Example: cdept(‘benzene’) nt = 1,000 au followed by rttmp(‘C13’) and rttmp(‘dept’) to process the |

| | |spectra. |

|cosy |55 |“cosy” This command sets up the parameters for a cosy experiment. |

|cosyps |55 |“phase sensitive cosy” This command sets up a phase sensitive cosy experiment. |

|ct |61 |“collected transients” This parameter indicates the number of transients that were actually collected. |

|ctext |62 |“clear text” This command clears the text from the current experiment. |

|cz |64 |“clear integral reset points” This command removes currently defined integral reset points. |

|d1, d2 |64 |“delay” These commands set the first and second delay times. These are used in nontrivial experiments to allow/prevent NOE effects, to allow spin evolution, etc. They are only |

| | |needed for gated decoupling and “named” experiments. |

|da |66 |“display arrays of acquisition parameters” This command displays the arrayed acquisition parameters. Example: pw = 20, 40, 60, 80 ga da would yield an array of four stacked spectra|

| | |differing in the pulse widths used. |

|dc |67 |“drift correct” This command levels the baseline with the lvl and tlt parameters, (i.e., a liner baseline correction). |

|dconi |69 |“display interactive contour plot” This command displays an interactive contour plot. |

|delta |77 |This parameter measures the frequency difference between the two cursors. Example: delta? asks what the delta value is. |

|dept |77 |“DEPT” This command sets up the parameters for a Distortionless Enhancement by Polarization Transfer experiment (used to distinguish CH3 from CH2 from CH groups). |

|deptproc |78 |“DEPT process” This command automatically processes DEPT data. |

|df |79 |“display fid” This command displays the current FID. [dfid is the same command.] |

|dg |85 |“display group of parameters” This command updates the parameter list and presents it as a window. |

|dga |85 |“display group of spin simulation parameters” This command displays the table of spin simulation parameters. |

|dgs |86 |“display group of special parameters” This command presents the list of special parameters which includes the shim settings, etc. |

|dli |89 |“display list of integrals” This command lists integrals and their reset points. |

|dll |90 |“display list of lines” This command displays a list of line frequencies and amplitude above the threshold. |

|dm |91 |“decoupler mode” This command turns the decoupler on or off. It is set at y or yyy or n or nnn if decoupler is always on or off. For “gated” experiments, dm = nny, nyn, yyn, etc. |

|dmf |93 |“decoupler modulation frequency” This command sets the modulation frequency for the WALTZ decoupling (i.e., broadband decoupling, dmm = W) Don’t play with this parameter!. |

|dmm |97 |“decoupler modulation mode” This command sets the type of decoupling. dmm = c for continuous wave (selective) decoupling, = W for broadband (WALTZ) decoupling, and = f and = r for |

| | |swept square wave and square wave decoupling, respectively. dmm = C or W are all we use. |

|dn |100 |“decoupler nucleus” This command sets up to decouple the specified nucleus (e.g., 1H, 19F, 31P) by looking up drfq and dof from lookup tables. |

|dof |101 |“decoupled offset” This command sets the decoupler offset (i.e., the center of the frequency to be decoupled). Use the sd command to set dof to the cursor position. |

|dp |104 |“double precision” This command can be set at ‘y’ of ‘n’. You should always have dp = ‘y’ to give the maximum wordlength and quality of data. |

|dpf |105 |“display peak frequencies” This command displays the peak maxima. |

|dps |107 |“display pulse sequence” This command displays the pulse sequence. |

|dpwr |107 |“decoupler power” This command sets the decoupler power. Has values of 0 to 63 in steps of 0.5 dB. Typical values are 8 dB for Waltz decoupling of 1H and 32 to 38 dB for selective |

| | |homonuclear decoupling of 1H. Never use dpwr of greater than 49 for dmm = ‘c’, ‘f’, or ‘r’. It can damage probe. |

|dqcosy |111 |“double quantum filtered cosy” This command sets up the parameters for this experiment. |

|dres |113 |“display resolution” This command displays the peak width at half-height of the peak on which the cursor is positioned. |

|ds |114 |“display spectrum” This command displays the current spectrum. |

|dscale |117 |“display scale” This command puts the scale on the screen. Examples: dscale and dscale(30) puts scale on screen at bottom and with a vp = 30, respectively. |

|dsn |120 |“display signal to noise” This command gives the S/N ratio between the largest peak in the window and the noise between the cursors (delta should = 200 Hz). |

|dssa |123 |“display stacked spectra offset” This command displays stacked spectra with an incremental offset. |

|dssh |125 |“display stacked spectra horizontal” This command displays a “normal” stacked plot. |

|e |129 |“eject” This command ejects the sample currently in the NMR. |

|ernst |136 |“calculate ernst angle pulse width” This command calculates the optimum pulse width to use to get the best S/N in a set time, the ernst angle. This value is always less than a 90( |

| | |pulse and depending on T1 is usually for a 10-45( pulse. The correct value for this allows you to pulse as quickly as possible with the best balance of relaxation between pulses. |

|exit |138 |“exit” This command exits VNMR. |

|f19 |144 |“automated 19F” This command automatically sets up the parameter for 19F data acquisition |

|FID | |“free induction decay” This term describes the “raw” NMR data set (i.e., in the time domain) and looks like series of superimposed sine waves. It is a measure of the magnetization |

| | |perpendicular to the magnetic field. It has “real”: and “imaginary” components that can be displayed separately and can be thought of as the magnetization in the x and y dimensions. |

| | |An FID is fourier transformed to give a “spectrum” of frequencies. |

|fn |154 |“fourier number” This command sets up the number of points to be transformed. It must be a power of two (i.e., 2n) but it will round itself up to the correct value, (e.g. 32,000 to |

| | |32,768). For fn = np, all the points are transformed. For fn < np only fn points are transformed. For fn> np, fn - np zeros are added to the data before it’s transformed. Such |

| | |zero filling yields increased resolution with no increase in signal to noise. A typical setting for zero filling is fn = 2np. |

|ft |159 |“fourier transform” This command says Fourier transform the current FID. |

|ga |175 |“ga” This command says go collect the experiment then wft the result. |

|gain |175 |“gain” This command sets the amplifier gain. Gain values range from 0 to 30 dB in steps of 2. Examples: gain = 20 and gain = ‘n’ sets the gain at 30 and as autogain, respectively.|

|gf |183 |“gausion function” This parameter in seconds, sets the Gausian apodization, “fudge factor,” for peak width often a wft. Examples: gf = ‘n’ and gf = 1 sets the data processing |

| | |parameter off and to 1 second, respectively. Normally, gf = ‘n’. |

|gfs |184 |“gausian shift” This parameter shifts the center of the Gausian apodization function into the spectrum. Examples: gfs = ‘n’ and gfs = 1 sets the gausian shift at off and 1 second, |

| | |respectively. |

|go |186 |“go” This command says go and collect the experiment. |

|h1 |195 |“automated 1H” This command automatically sets up the parameters for 1H data acquisition |

|hc |197 |“automated 1H and 13C” This command combines automated 1H and 13C data acquisition setup. |

|hcapt |197 |“automated 1H, 13C and APT” This command sets up for collection of all three parameters. |

|hccorr |198 |“automated 1H, 13C, and HETCOR” This command sets up the parameters for carrying out all three experiments. |

|hcdept |198 |“automated 1H, 13C, and Dept” This command sets up the parameters for automated running of all three experiments. |

|hcosy |199 |“automated 1H and COSY” This command sets up parameters for automated 1H and COSY collection |

|hetcor |200 |“HETCOR” This command sets up the parameters for a 1H-13C HETCOR experiment. You must already have collected a 1H spectrum. |

|ho |201 |“horizontal offset” This parameter sets the horizontal offsets of stacked plot. vo sets vertical offsets of 1-D data. |

|homadj |202 |“homonuclear 2-D J-resolved” This command sets up the parameters for homonuclear 2-D J-resolved spectra. |

|i |207 |“insert” This command inserts the sample into the NMR. |

|inset |215 |“inset” This command displays the part of the spectrum between two cursors as an inset. |

|integrate |215 |“automatically integrate” This command automatically integrates the spectrum. |

|jexpx | |jumps to experiment x |

|killplot |219 |“kill plot” This command kills all plots in the queue. |

|killprint |219 |“kill print” This command kills all print jobs in the queue. |

|lb |222 |“line broadening” This parameter is the number one “fudge factor,” apodization function, used in weighted fourier transforms. A lb value equal to 1 Hz is conventional and “hides” |

| | |small shiming errors. lb = ‘n’ turns it off. |

|lock |229 |“lock” This command performs an automatic lock. |

|lp |233 |“1st order phase” This parameter sets the frequency dependent component of the phasing (rp is the consant component). lp has no effect at the right hand edge of the spectrum. |

|lsfid |241 |“left shift fid” This parameter left shifts the FID. In other words, which points in the FID won’t be fourier transformed. Example: lsfid = 50 does not transform the first 50 |

| | |complex points of the spectrum. (i.e., left shift 50 points). |

|lvl |244 |“level” This parameter specifies the amount of the linear baseline correction (turned on by dc). |

|movesw |257 |“move sweep width” This command moves the transmitter offset frequency, tof, to the middle of the window defined by the two cursors and changes the sweep width, sw, to the difference|

| | |between the two cursors. In practice if you use the left and right hand cursors to mark the edges of a spectral window you’d like to collect data from then type movesw the sw and tof|

| | |values will be automatically set to do this. It is good, or at least “neat”, practice to manually change sw to some even multiple of ppm (i.e., 10 ppm or 100 ppm). To do this type |

| | |sw = 10 p or sw = 100 p, respectively. |

|movetof |257 |“move transmitter offset frequency” This command moves the transmitter offset frequency, tof, to the current position of the cursor. |

|mp(x,y) | |“move parameter” This command moves the experimental parameters from experiment x to y. |

|nl |264 |“nearest line” This command moves the cursor to the top of the nearest peak. |

|noesy |266 |“NOESY” This command sets up the NOESY experiment. |

|np |268 |“number of points” This parameter is the product of the acquisition time and the scan width (np = 2 x at x sw). It has a maximum value of 32 K for single precision and 64 K for |

| | |double precision due to hardware and software limits on the data system. Its value changes automatically as you change at and sw. Example: np = 64,000 sets at and sw to conform |

| | |the 64,000 maximum. |

|nt |269 |“number of transients” This parameter sets the maximum number of transients to be collected in a spectrum. The signal to noise ratio increases proportional to the square root of the|

| | |number of transients (really, it is even slower than this and a value of (.7 (nt)0.5 is not unreasonable). Example: nt = 32 sets the number of transients as 32. |

|p31 |276 |“31P” This command sets up normal31P NMR parameters. |

|page |278 |“page” This command says print the previous list of stuff all on one page and do it now, sends data to the printer. Example: pl pscale pap page would print a spectrum, its scale, |

| | |and parameters on one page. |

|pap |279 |“print all parameters” This command tells the system to print all the parameters (i.e., those given by dg). Requires a “page” command. |

|pl |296 |“plot” This command sets up the current spectrum to plot. Requires a “page” command to print. Examples: pl and pl (80) would plot a spectrum at the page bottom and with a vp of |

| | |80, respectively. |

|plapt |200 |“plot apt” This command plots apt spectrum (can do this on same page as 13C spectrum). |

|plarray |300 |“plot array” This command plots an array of 1-D spectra. |

|plc |300 |“plot 13C” This command plots 13C spectra. |

|plcosy |301 |“plot cosy and noesy” This command plots 2-D homocorelation spectra. |

|pldept |302 |“plot dept” This command plots dept data. |

|plfid |302 |“plot FID” This command plots the current FID. Requires a page command. |

|plh |303 |“plot 1H” This command plots 1H spectra. |

|plhxcor |303 |“plot HETCOR” This command plots hetcor spectra. |

|pll |305 |“plot line list” This command plots the line list. |

|plot |306 |“generic plot” This command calls up the correct plot macro. |

|ppa |311 |“plot parameters” This command plots all parameters in plain English (cf pap). |

|ppf |312 |“plot peak frequencies” This command plots these positions over the peaks. |

|pps |313 |“plot plus sequence” This command plots the pulse sequence (cf dps). |

|procarray |317 |“process array” This command processes arrayed FIDs. |

|process |318 |“generic automatic processing” This command automatically picks the correct data processing macro and does it. |

|pscale |320 |“print scale” This command tells the system to print a scale. It requires a “page” command. Examples: pscale and pscale (80) request scales to be printed on the bottom of the page|

| | |and with a vp of 80, respectively. |

|pwd |326 |“print working directory” This command displays where you are in your hierarchy of files. |

|ra |332 |“resume acquisition” This command resumes data acquisition where it left off. |

|resolu |338 |“set resolution enhancement” This command calculates default resolution enhancement functions (e.g., lb and gr) including zero filling. |

|rl |344 |“reference line” This command defines the current cursor position as the reference line. It is used to “zero” the scale, usually on the peak of TMS or the solvent. Examples: |

| | |rl(2.32p) and rl(487) define the two cursor positions as 2.32 ppm and 487 Hz, respectively. |

|rp |347 |“right phase parameter” This parameter in the phase term that is frequency independent. (lp is the frequency dependent part.) |

|rts | |“retrieve shims” This command retrieves the shim settings recorded in the shims menu. You are promoted to name the specific shim settings to use. On the 5 mm probe these are |

| | |usually stored as “best” or “best5”. Example: rts return best 5 return retrieve the shim settings in “best5” and loads them into the spectrometer. |

|rttmp |349 |“retrieve data from a subfile” This command retrieves subfiles. Examples: rttmp(‘H1’) and rttmp(‘dept’) would retrieve the 1H and dept data, respectively. |

|s |351 |“save screen setup s1, s2, s3, etc.” These commands save the current screen set ups as 1, 2, 3, etc. r1 retrieves the set up defined by s1. |

|sa |352 |“stop acquisition” This command temporarily stops data acquisition. ra resumes it and aa permanently stops it. |

|sb |353 |“sinebell” This parameter is for the sinebell apodization correction, “fudge factor,” for the wft. Typically, sb = ‘n’. Normally used in absolute value 2-D experiments only. |

|sbs |354 |“shift sinebell” This parameter is the shift of the sinebell apodization, “fudge factor”. |

|sc |355 |“start of chart in x axis” This parameter positions the start of the plotting position on the paper with respect to its right edge. |

|sc2 |355 |“start of chart in y axis” This parameter sets sc for th y axis of the paper (from the bottom?). |

|sd |357 |“set decoupler” This command sets the decoupler offset, dof, to the current cursor position. |

|sda |358 |“set decoupler array” This command sets up an array of decoupler offsets (use sd for first position and sda for subsequent positions). |

|sf |373 |“start of FID” This parameter gives the start of the displayed portion of the FID. |

|sfrg |373 |“sweep frequency” This parameter is chosen by the computer to correspond to the selected observe nucleus. |

|shim |374 |“autoshim” This command runs an autoshim experiment. |

|sp |382 |“start of plot” This parameter gives the starting position, on the right hand side, of the spectrum on the display window. Examples: sp = 231 or sp = 1.13p sets the starting point |

| | |at 231 Hz or 1.13 ppm, respectively. |

|ss |389 |“steadystate” This command causes data to be accumulated only for the steady state pulses. |

|su |395 |“set up” This command resets the communication between the host computer and the NMR console. Do this every time you change the observe nucleus, decoupling procedures, pulse |

| | |sequence, etc. It ensures that both the host computer and the NMR console are “in sinc”. |

|svf |397 |“save FID” This command tells the system to save the current FID data. The system prompts you for a name. |

|svp |398 |“save parameters” This command tells the system to save the current parameters as a defined experiment. It will prompt you for a name. |

|svs |398 |“saves shim settings” This command saves the current shim settings in the shim menu. The system prompts you to name the current set of shims. |

|sw |400 |“sweep width” This parameter sets the width of the window that the spectrometer will observe centered around the transmitter offset frequency (tof). When you don’t know exactly how |

| | |wide a spectrum will be or where it will be centered, collect a quick spectrum at a wide sw to be sure it includes all the peaks. Then, transform it and use the cursors and movesw to|

| | |set a window that just includes all the peaks. This gives a minimum sw which, in turn, yields a minimum np and so allows you to get the longest at and hence the best resolution. |

| | |Example: sw = 34,000 sets the sweep width at 34,000 Hz. |

|temp | |“temperature” This command sets the temperature of a variable temperature run. It shouldn’t be changed more than 20 degrees at a time. Example: temp = -20 and temp = ‘n’ sets |

| | |variable temperature at -20(C and off, respectively. |

|th |410 |“threshold” This command sets the threshold for peak picking |

|time |412 |This parameter asks how long the current experiment will take to collect. Example: time? asks how long it will take. |

|tn |413 |“transmitter nucleus” This command indicates the selected transmitter nucleus. |

|tof |414 |“transmitter offset frequency” This parameter sets the center of the transmitter window (i.e., the center of the sweep width, sw). This is the frequency at which the observe nucleus|

| | |is pulsed. The compound movetof is used to move the transmitter frequency, tof, to the position of the cursor. The tof is sometimes observable in the middle of the spectrum as a |

| | |weak “unphased” signal. If it overlaps with a signal of interest, it should be moved away. Example: tof = -486 means the transmitter is offset -486 Hz from the default value |

| | |(defined by the software for a given solvent with respect to its deuterium lock signal). |

|tuneoff |421 |“tuning off” This command stops the pulsing used during tuning. The cables are moved back from the meter after this command is used. “btune” starts tuning. |

|vp |431 |“vertical position” This command established the height of the baseline. It is usually at zero for conventional 1-D spectra. Example: vp = 80 positions the baseline in the middle |

| | |of the page. |

|unlock | |“unlock” This command unlocks experiments, e.g., unlock(2) unlocks experiment #2 |

|vs |431 |“vertical scale” This parameter sets the “height” of the spectrum. A vertical scale of 160 is just right to keep all peaks on the screen. Example: vs = 160 sets the vertical scale|

| | |at 160. |

|wc |436 |“width of chart” This parameter sets the width of the paper, the plotter area. |

|wc2 |436 |“width of chart in y” This parameter = wc for y axis. |

|wf |438 |“width of fid” This parameter gives the width of FID to be displayed. |

|wft |438 |“weighted fourier transform” This command weights the FID with various “fudge factors” prior to fourier transforming them. |

|wp |443 |“width of plot” This parameter gives the width of the spectrum on the display window. You should always use standard values for this parameter (e.g., 8 ppm, 4 ppm, 2 ppm, 0.5 ppm, |

| | |40 Hz, 20 Hz, 10 Hz, 5 Hz) to make later comparison of spectra much more convenient. Examples: wp = 40 or wp = 2p sets the width of plot at 40 Hz or 2 ppm, respectively. |

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