Programs of the NMRPipe System
Var2Pipe: Varian to NMRPipe-Format Conversion

  var2pipe hdrFlags < varData > pipeFile
General Flags:
Flag Argument Default Description
 -in inName Varian Input.
 -out outTemplate NMRPipe Output.
 -ov Force Overwrite.
 -nofs No File Size Check.
 -nodir Suppress Creation of Directory.
 -verb Verbose Mode On.
Byte-Swap Options:
 -swap Do Four-Byte Swap (Default).
 -noswap Suppress Four-Byte Swap.
 -aswap Suppress Four-Byte Swap. (Meaning is System-dependant)
 -noaswap Do Four-Byte Swap. (Meaning is System-dependant)
Varian Header Flags:
 -hdr Use Varian Header Data (Default).
 -nohdr Don't Use Varian Header.
 -hw hSize 8 Header Size in Four-Byte Words.
 -pw pSize 7 Pad Size in Four-Byte Words.
 -info Show Header Info on stdout, Don't Convert Data.
Options Set Via Varian Header:
 -i2r Convert Integer to Real.
 -noi2r No Integer to Real Conversion.
 -short Input is Two-Byte Data.
 -long Input is Four-Byte Data.
 -dsp Input is floating-point DSP data (Same as -noi2r).
Parallel Processing (Not Implemented):
 -par sListName Server List File Name.
 -first firstPlane First Plane to process.
 -last lastPlane Last Plane to process.

General Header Arguments:
 -fdata loc val... Adjust File Header.
 -u1 -u2...-u5 User Parameters.
 -ndim Number of Dimensions.
 -tau Tau Value.
 -day Day.
 -month Month (1-12).
 -year Year.
 -hours Hours (0-23).
 -mins Minutes (0-59).
 -secs Seconds (0-59).
 -temp Temperature, Degrees C.
 -aq2D 2D Acquisition Code or Keyword:
 -pipeFlag 0=Multi-File Data.
  1=Pipeline Stream or Single File.
 -tpFlag 0=Not Transposed.

Header Labels:
 -srcName Source File Name.
 -operName Operator Name.
 -userName User Name.
 -comment Comment.
 -title Title.

Axis-Specific Header Flags -x.. -y.. etc:
Default Values are zero:
 -xN Actual Size in File Pts Real + Imag.
 -xT Current Time Domain Size Pts Real or Imag.
 -xSW Full Spectral Width Hz.
 -xOBS Observe Frequency MHz.
 -xCAR Carrier Position ppm.
 -xLAB Axis Label 8 Chars, No Spaces.

 -xMODE Acquisition Mode Code or Keyword:

 -xALT Sign Adjustment Code or Keyword:
  0=Complex,States No Alternation Needed.
  0=Real,TPPI No Alternation Needed.
  1=Sequential,Bruker Real Alternation.
  2=States-TPPI Complex Alternation.
  With Negation of Imaginaries:
  16=Complex-N No Alternation Needed.
  16=States-N No Alternation Needed.
  18=States-TPPI-N Complex Alternation.

Note: Default Sign Adjustment Mode is Automatically
Set by the Corresponding Acquisition Mode Keyword.

Axis-Specific Header Flags -xQ -yQ etc. Not required for conversion. Used to adjust header:
 -xTD Original Time Domain Size. Pts.
 -xFD Final Max Freq Domain Size. Pts.
 -xZFP Zero Fill Parameter. Pts (Negative).
 -xMID Carrier Virtual Loc. Pts.
 -xORIG Last Point Coord. Hz.
 -xDIM Dimension Order.
  2=Original X-Axis
  1=Original Y-Axis
  3=Original Z-Axis
  4=Original A-Axis
 -xFT Fourier Flag Code or Keyword:
  0=Time Time-Domain Data.
  1=Freq Frequency-Domain Data.

Special Acquisition-Axis Flags (no longer required):
 -aqN Actual Size. Pts Real or Imag.
 -aqMODE Acquisition Mode. 0=Complex.

Axis-Specific Processing Values -xQ -yQ etc:
 -xAPOD Apodize Function SP EM GM TM TRI or NONE.
 -xQ1 Apodize Parameter 1. Depends on Function.
 -xQ2 Apodize Parameter 2. Depends on Function.
 -xQ3 Apodize Parameter 3. Depends on Function.
 -xC1 First Point Scale. Default is 1.0.
 -xP0 Zero Order Phase. Degrees.
 -xP1 First Order Phase. Degrees.

Special Varian Format Flags:
 -sign Use Sign Adjustment (Default).
 -nosign Suppress Sign Adjustment.

 -aqORD aqOrd 0 Acquisition Order Code.
  0 = 2D d2,phase
  0 = 3D d3,d2,phase2,phase
  0 = 4D d4,d3,d2,phase3,phase2,phase
  1 = 3D d3,d2,phase,phase2
  1 = 4D d4,d3,d2,phase,phase2,phase3
  2 = 4D d3,d2,d4,phase3,phase2,phase

  1. 4D Conversion requires explicit input file
  as specified by the -in argument.
  2. By default, byte-swap is ON for Pentium systems,
  and OFF for other platforms.

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