nmrdrawlab1 - 1 Introduction to nmrPipe F.Delaglio, S....

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1 Introduction to nmrPipe F.Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfiefer, and A. Bax. J. Biomol. NMR, 6 (1995) 277-293 Web site: spin.niddk.nih.gov/bax/software/NMRPipe Requirements: UNIX operating system ( SGI, SUN, Linux, MAC OSX, etc.) Basic description: From the manual- “The nmrPipe program is the central part of a system of tools for multi-dimensional spectral processing using UNIX pipes.” The nmrpipe data processing program consists of a number of functions ( e.g. FT ) that are linked together via unix pipes. Unix pipe example: ls | more The vertical line is a 'pipe' ; the output of the list files command ( ls ) becomes the input of the screen paging command ( more). The functions are usually strung together in a script or macro and executed as a single unix command. A second program called 'nmrDraw' is used to visualize the processed nmr data. This program provides basic functions such as drawing contours, vertical or horizontal traces, peak picking, integration, etc. A number of functions are available in menus ( and mapped to the keyboard) to allow for quick manipulation of the data for analysis. One can also use other programs to visualize the data ( e.g. nmrview). There are also other programs such as 'var2pipe' which are used to convert data into nmrpipe format. The program manual pages are filled with information and examples. ( man nmrPipe ) Brief descriptions of specific functions are accessible via nmrPipe - 'nmrPipe -help ' will list most functions. 'nmrPipe -fn GM -help' will give description of the GM function for example.
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2 Converting spectrometer data into nmrPipe format: First convert data from spectrometer format ( Varian, Bruker, etc.) to nmrpipe format using conversion scripts. This is most easily done using a built-in program called 'varian' for Varian data ( or 'bruker' for Bruker data). Our first example will be a 1d proton spectrum using a Varian dataset called 'sample1d.fid'. -open a terminal window and copy this dataset into your home directory. 1) cd into sample1d.fid, then type 'varian' – this starts a tcl/tk script and brings up these two windows: 2) Click on the 'Read Parameters' button. The script will read the parameter file ( 'procpar') from inside the sample.fid directory and update the parameters to give:
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3 Note that the template now shows only a single dimension file, with the appropriate paramters. At this stage, one can update the center position PPM value if known – this can also be done later. 3) Click on 'Save Script', and the 'Execute Script'. These actions have created an executable unix shell script called 'fid.com' which is displayed in the lower window, and executed it. The script shows that a program called 'var2pipe' is run with a variety of arguments; the input file is 'fid' , the generic name for the raw varian binary data, and the output is 'test.fid', which is now in nmrpipe format. Since we started the 'varian' program inside the sample1d.fid directory, all these files
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nmrdrawlab1 - 1 Introduction to nmrPipe F.Delaglio, S....

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