Programs of the NMRPipe System
bruk2pipe: Bruker to NMRPipe-Format Conversion.

  bruk2pipe hdrFlags < brukSER > pipeFile
General Flags:
Flag Argument Default Description
 -in inName Bruker SER Input.
 -out outTemplate NMRPipe Output.
 -mem memMB 0 MByte Memory Buffer. (Use 0 for Auto)
 -ov Force Overwrite.
 -noext No Extract Performed (Default).
 -ext Extract Valid Points Only.
 -nodir Suppress Directory Creation.
 -nofs Suppress File Size Check.
 -verb Verbose Mode On.
Format Flags:
 -AMX SER is Bruker AMX Data (Default).
 -DMX SER is Bruker DMX Data. (Requires -decim flag.) (Implies -ext flag.)
 -AM SER is 3-Byte Bruker AM Data.
 -bo bOff 0 Byte Offset for Input. Commonly 768 to skip AM header.
 -bad bPt 8e6 Bad Point Threshold (Use 0.0 for None).
Byte-Swap Options:
 -swap Do Four-Byte Swap.
 -noswap Suppress Four-Byte Swap (Default).
 -aswap Suppress Four-Byte Swap. (Meaning is System-dependant)
 -noaswap Do Four-Byte Swap. (Meaning is System-dependant)
Special Digital Filter Parameters from 'acqus':
 -grpdly gV 0.0 Bruker GRPDLY Value.
 -decim dV 0 Bruker DECIM Value.
 -dspfvs fV 10 Bruker DSPFVS Value, 10-13,20-23. Default = 11 for DQD mode.
 -c cV 1.0 First/Last Point Scale.
 -skip sV 4 Points to Skip in Head Correction. (Use -1 for No Correction)
 -zf Temporary Zero Fill for Speed. (Default)
 -nozf No Temporary Zero Fill.
  By default, byte-swap is OFF for Pentium systems, and ON for other platforms.
General Header Arguments:
 -fdata loc val ... Adjust File Header.
 -u1 u1 0.0 User Parameter 1.
 -u2 u2 0.0 User Parameter 2.
 -u3 u3 0.0 User Parameter 3.
 -u4 u4 0.0 User Parameter 4.
 -u5 u5 0.0 User Parameter 5.
 -ndim ndim 0 Number of Dimensions.
 -tau tau 0 Tau Value.
 -day day 0 Day.
 -month month 0 Month (1-12).
 -year year 0 Year.
 -hours h 0 Hours (0-23).
 -mins m 0 Minutes (0-59).
 -secs s 0 Seconds (0-59).
 -temp t 0.0 Temperature, Degrees C.
 -aq2D aq2D 0 2D Acquisition Code or Keyword: 0=Magnitude. 1=TPPI. 2=States. 3=Image.
 -pipeFlag pipeFlag 0 0=Multi-File Data. 1=Pipeline Stream or Single File.
 -tpFlag tpFlag 0 0=Not Transposed. 1=Transposed.
Header Labels:
 -srcName src Source File Name (16 Characters Max).
 -operName oper Operator Name (32 Characters Max).
 -userName user User Name (16 Characters Max).
 -comment comment Comment (160 Characters Max).
 -title title Title (60 Characters Max).
Axis-Specific Header Flags -x.. -y.. etc:
 -xN xN 0 Actual Size in File Pts Real + Imag.
 -xT xT 0 Current Time Domain Size Pts Real or Imag.
 -xSW xSW 0.0 Full Spectral Width Hz.
 -xOBS xOBS 0.0 Observe Frequency MHz.
 -xCAR xCAR 0.0 Carrier Position ppm.
 -xLAB xLAB None Axis Label 8 Chars, No Spaces.
 -xMODE xMODE 0 Acquisition Mode Code or Keyword: 0=Complex,States,Complex-N,States-N. 0=States-TPPI,States-TPPI-N. 1=Real,TPPI. 2=Sequential,Bruker.
 -xALT xALT 0 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.

Axis-Specific Header Flags -xQ -yQ etc. Not required for conversion. Used to adjust header:
 -xTD xTD Original Time Domain Size. Pts.
 -xFD xFD Final Max Freq Domain Size. Pts.
 -xZFP xZFP Zero Fill Parameter. Pts (Negative).
 -xMID xMID Carrier Virtual Loc. Pts.
 -xORIG xORIG Last Point Coord. Hz.
 -xDIM xDIM Dimension Order. 2=Original X-Axis 1=Original Y-Axis 3=Original Z-Axis 4=Original A-Axis
 -xFT xFT Fourier Flag Code or Keyword: 0=Time Time-Domain Data. 1=Freq Frequency-Domain Data.
Special Acquisition-Axis Flags (no longer required):
 -aqN aqN Actual Size. Pts Real or Imag.
 -aqMODE aqMODE Acquisition Mode. 0=Complex. 1=Real. 2=Sequential.
Axis-Specific Processing Values -xQ -yQ etc:
 -xAPOD xAPOD Apodize Function SP EM GM TM TRI or NONE.
 -xQ1 xQ1 Apodize Parameter 1. Depends on Function.
 -xQ2 xQ2 Apodize Parameter 2. Depends on Function.
 -xQ3 xQ3 Apodize Parameter 3. Depends on Function.
 -xC1 xC1 First Point Scale. Default is 1.0.
 -xP0 xP0 Zero Order Phase. Degrees.
 -xP1 xP1 First Order Phase. Degrees.

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