Spectra Format Conversion from NMRPipe Data: Difference between revisions

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 '''Spectra Format Conversion from NMRPipe Processed Data'''  
'''Spectra Format Conversion from NMRPipe Processed Data'''  


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===== NMRPipe to Sparky  =====
===== NMRPipe to Sparky  =====


For a 2D Matrix name nmrpipe_2d-data.ft2  
:Type the following command in the UNIX terminal
::For a 2D dataset 'gnhsqc.ft2' ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_2D_Experiment])


:pipe2ucsf nmrpipe_2d-data.ft2 sparky_2d-data.ucsf
:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D&nbsp;<sup>15</sup>N and&nbsp;<sup>13</sup>C-edited Experiments])
 
:::Use xyz2pipe to combine 2D planes into one single PIPE file (Go to the directory where the 3D planes are stored)
 
::::xyz2pipe -in test%03d.ft3 -x &gt; 3D_HNCO.mat
 
:::Convert the single PIPE file to UCSF format
 
::::pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf
 
:Additional information can be found in [http://www.cgl.ucsf.edu/home/sparky/manual/index.html Sparky Manual] <ref>T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco </ref>


===== NMRPipe to CARA  =====
===== NMRPipe to CARA  =====
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:At the end of the processing script (e.g. ft2d.com or nmrproc.com), insert the following two lines:  
:At the end of the processing script (e.g. ft2d.com or nmrproc.com), insert the following two lines:  
::nmrPipe -in gnhsqc.ft2 \  
::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])
::pipe2xyz -nv -out filename.nv
:::
:::nmrPipe -in gnhsqc.ft2 \  
:::|pipe2xyz -nv -out filename.nv
 
::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_Processing_Procedure_for_3D_15N_and_13C-edited_Experiments Routine Processing Procedure for 3D&nbsp;<sup>15</sup>N and&nbsp;<sup>13</sup>C-edited Experiments])
:::
:::xyz2pipe -in lp/test%03d.ft3 -x \
:::|pipe2xyz -nv -out filename.nv
 
===== References  =====
 
<references /> <br> <br> <br> Updated by Hsiau-Wei Lee, 2011

Latest revision as of 20:11, 26 January 2023

Spectra Format Conversion from NMRPipe Processed Data


NMRPipe to Sparky
Type the following command in the UNIX terminal
For a 2D dataset 'gnhsqc.ft2' ([1])
pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
For a 3D dataset (Routine Processing Procedure for 3D 15N and 13C-edited Experiments)
Use xyz2pipe to combine 2D planes into one single PIPE file (Go to the directory where the 3D planes are stored)
xyz2pipe -in test%03d.ft3 -x > 3D_HNCO.mat
Convert the single PIPE file to UCSF format
pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf
Additional information can be found in Sparky Manual [1]
NMRPipe to CARA

NMRPipe to XEASY
NMRPipe to NMRViewJ
At the end of the processing script (e.g. ft2d.com or nmrproc.com), insert the following two lines:
For 2D dataset (Routine Processing Procedure for 2D Experiment)
nmrPipe -in gnhsqc.ft2 \
|pipe2xyz -nv -out filename.nv
For a 3D dataset (Routine Processing Procedure for 3D 15N and 13C-edited Experiments)
xyz2pipe -in lp/test%03d.ft3 -x \
|pipe2xyz -nv -out filename.nv
References
  1. ↑ T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco




Updated by Hsiau-Wei Lee, 2011

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