Welcome: an Introduction to this Site
NMRPipe: a Comprehensive Software System for Biomolecular NMR
Special Applications: NMR Drug Screening, Automation, and so on
Dipolar Couplings, Chemical Shifts, and Protein Structure
Miscellaneous

Frank's CV, Recent Slides, and Thesis

 

  

 

  Frank Delaglio, Ph.D.

   Software Science Consultant
  13840 Grey Colt Drive
  North Potomac MD 20878 USA

  Tel: 301 806-0867
  Fax: 301 309-8717
  E-mail: delaglio@nmrscience.com



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.
Notes:
  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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last updated: Jan 22, 2009 / big frank

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