Spectra Format Conversion from NMRPipe Data - Revision history

Suryaven at 20:11, 26 January 2023

2023-01-26T20:11:50Z

← Older revision		Revision as of 20:11, 26 January 2023
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	:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf		:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
	::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/~~wiki~~/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])		::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)
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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:
	::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/~~wiki~~/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])		::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/~~wiki~~/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])		::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 \

Suryaven at 20:09, 26 January 2023

2023-01-26T20:09:37Z

← Older revision		Revision as of 20:09, 26 January 2023
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	:Type the following command in the UNIX terminal		:Type the following command in the UNIX terminal
	::For a 2D dataset 'gnhsqc.ft2' ([~~http~~://~~www~~.~~nmr2~~.buffalo.edu/~~wiki~~/Routine_2D_Experiment ~~Routine Processing Procedure for 2D Experiment~~])		::For a 2D dataset 'gnhsqc.ft2' ([https://nesgwiki.chem.buffalo.edu/index.php/Routine_2D_Experiment])

	:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf		:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf

Suryaven at 02:09, 26 January 2023

2023-01-26T02:09:08Z

← Older revision		Revision as of 02:09, 26 January 2023
Line 9:		Line 9:

	:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf		:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
	::For a 3D dataset ([~~http~~://~~www~~.~~nmr2~~.buffalo.edu/wiki/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])		::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/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 ([~~http~~://~~www~~.~~nmr2~~.buffalo.edu/wiki/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])		::For 2D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/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 ([~~http~~://~~www~~.~~nmr2~~.buffalo.edu/wiki/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])		::For a 3D dataset ([https://nesgwiki.chem.buffalo.edu/wiki/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 \

Hlee at 01:16, 18 August 2011

2011-08-18T01:16:13Z

← Older revision		Revision as of 01:16, 18 August 2011
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	===== References =====		===== References =====

	<references/>		<references /> <br> <br> <br> Updated by Hsiau-Wei Lee, 2011

Hlee at 20:28, 7 December 2009

2009-12-07T20:28:26Z

← Older revision		Revision as of 20:28, 7 December 2009
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	===== References =====		===== References =====

	~~<~~references/~~>~~		<references/>

Hlee at 20:27, 7 December 2009

2009-12-07T20:27:37Z

← Older revision		Revision as of 20:27, 7 December 2009
Line 40:		Line 40:
	===== References =====		===== References =====

	<~~reference~~/>		<references/>

Hlee at 20:27, 7 December 2009

2009-12-07T20:27:10Z

← Older revision		Revision as of 20:27, 7 December 2009
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	::::pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf		::::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]		: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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	:::xyz2pipe -in lp/test%03d.ft3 -x \		:::xyz2pipe -in lp/test%03d.ft3 -x \
	:::\|pipe2xyz -nv -out filename.nv		:::\|pipe2xyz -nv -out filename.nv

			===== References =====

			<reference/>

Hlee at 20:25, 7 December 2009

2009-12-07T20:25:32Z

← Older revision		Revision as of 20:25, 7 December 2009
Line 18:		Line 18:

	::::pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf		::::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]

	===== NMRPipe to CARA =====		===== NMRPipe to CARA =====

Hlee at 20:21, 7 December 2009

2009-12-07T20:21:34Z

← Older revision		Revision as of 20:21, 7 December 2009
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	~~ ~~'''Spectra Format Conversion from NMRPipe Processed Data'''		'''Spectra Format Conversion from NMRPipe Processed Data'''

	<br>		<br>
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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' ([http://www.nmr2.buffalo.edu/wiki/Routine_2D_Experiment Routine Processing Procedure for 2D Experiment])

	:pipe2ucsf ~~nmrpipe_2d~~-~~data~~.~~ft2 sparky_2d~~-~~data~~.ucsf		:::pipe2ucsf gnhsqc.ft2 gnhsqc.ucsf
			::For a 3D dataset ([http://www.nmr2.buffalo.edu/wiki/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)

			::::xyz2pipe -in test%03d.ft3 -x > 3D_HNCO.mat

			:::Convert the single PIPE file to UCSF format

			::::pipe2ucsf 3D_HNCO.mat 3D_HNCO.ucsf

	===== 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 ([http://www.nmr2.buffalo.edu/wiki/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 ([http://www.nmr2.buffalo.edu/wiki/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 \
			:::\|pipe2xyz -nv -out filename.nv

Hlee at 16:28, 7 December 2009

2009-12-07T16:28:20Z

← Older revision		Revision as of 16:28, 7 December 2009
Line 1:		Line 1:
	'''Spectra Format Conversion from NMRPipe Processed Data'''		'''Spectra Format Conversion from NMRPipe Processed Data'''

			<br>

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

	For a 2D Matrix name nmrpipe_2d-data.ft2		For a 2D Matrix name nmrpipe_2d-data.ft2
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	:pipe2ucsf nmrpipe_2d-data.ft2 sparky_2d-data.ucsf		:pipe2ucsf nmrpipe_2d-data.ft2 sparky_2d-data.ucsf

	NMRPipe to CARA		===== NMRPipe to CARA =====

			===== <br> NMRPipe to XEASY =====

	NMRPipe to ~~XEASY~~		===== NMRPipe to NMRViewJ =====

	~~NMRPipe to NMRViewJ~~		: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 \
	::nmrPipe -in gnhsqc.ft2 \
	::pipe2xyz -nv -out filename.nv		::pipe2xyz -nv -out filename.nv