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
  325 Union Avenue #212
  Campbell CA 95008 USA


  Tel: 301 806-0867
  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.

[ Home ] [ Terms of Use ] [ Copyright ]
last updated: Jul 4, 2012 / big frank

Contact site designer mimi at mdelaglio@hotmail.com