Spectra Format Conversion from NMRPipe Data: Difference between revisions
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:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf | :::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf | ||
::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/ | ::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 <sup>15</sup>N and <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) | :::Use xyz2pipe to combine 2D planes into one single PIPE file (Go to the directory where the 3D planes are stored) | ||
| Line 28: | Line 28: | ||
: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: | ||
::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/ | ::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment]) | ||
::: | ::: | ||
:::nmrPipe -in gnhsqc.ft2 \ | :::nmrPipe -in gnhsqc.ft2 \ | ||
:::|pipe2xyz -nv -out filename.nv | :::|pipe2xyz -nv -out filename.nv | ||
::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/ | ::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 <sup>15</sup>N and <sup>13</sup>C-edited Experiments]) | ||
::: | ::: | ||
:::xyz2pipe -in lp/test%03d.ft3 -x \ | :::xyz2pipe -in lp/test%03d.ft3 -x \ | ||
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 2D dataset (Routine Processing Procedure for 2D Experiment)
- 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
- For a 3D dataset (Routine Processing Procedure for 3D 15N and 13C-edited Experiments)
References
- ↑ T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco
Updated by Hsiau-Wei Lee, 2011