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
bin2pipe: General-Purpose Four-Byte Binary Data to NMRPipe-Format Conversion.

  bin2pipe hdrFlags < binData > pipeFile
General Flags:
Flag Argument Default Description
 -in inName Four-Byte Binary Input.
 -in inNameR inNameI Four-Byte Binary Input Pair.
 -out outTemplate NMRPipe Output.
 -ov Force Overwrite.
 -nodir Suppress Directory Creation.
 -nofs Suppress File Size Check.
 -verb Verbose Mode On.
General Format Flags:
 -bo bytOff 0 Byte Offset at Start of Input.
 -bp bytPad 0 Bytes Between 1D Slices in Input.
 -pad Pad missing data by zeros.
 -nopad Suppress padding by zeros (Default).
 -il Interleave Pairs of Input Planes (Default if two inputs are given).
 -noil No Interleave of Input Planes (Default if one input is given).
 -i2r Do Int-to-Real Conversion.
 -neg Do Negation of Imaginary Data.
 -ri Do Separation of Real/Imag.
 -bad bPt 0.0 Bad Point Threshold (Use 0.0 for No Bad Point Adjust).
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)
Specific Format Flags:
 -alpha Same As: -bo 8704 -i2r -ri -neg -aswap
 -alpha2 Same As: -bo 16384 -i2r -ri -neg -aswap
 -lambda Same As: -bo -1 -ri -neg -aswap
 -gsx Same As: -ri -i2r -aswap
 -ex Same As: -ri -i2r -aswap
 -chem Same As: -i2r -aswap
 -ge Same As: -ri -noaswap
 -ftOLD Same As: -bo 8 -bp 12 -ri -pad -noaswap (Required byte offset may vary)
 -ftNEW Same As: -bo 1036 -bp 4 -ri -pad -noaswap (Required byte offset may vary)
Null Data Flags:
 -noIn No Input Data (Use Zeros).
 -noOut No Output Data (Header Only).
Parallel Processing: (Not yet 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 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.
Notes:
  1. JEOL GSX Phase-Sensitive input is specified as a pair of file names.
  2. JEOL LAMBDA mode (-lambda) will attempt to find the byte offset from the JEOL header.
  3. By default, byte-swap is ON for Pentium systems, and OFF for other platforms.

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last updated: Jan 22, 2009 / big frank

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