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drx2pipe ========== What the script does: --------------------- Automatically creates the conversion file for Bruker Avance data to NMRPipe(1) format for off-line processing. This makes the creation of the required file fast, trivial and error-free. It works by inspecting the acqus files and extracting the required parameters. It also has the advantage that additional information on the experiment such as the sign of peaks or indirect dimension phasing information can be stored in the header. The header already stores the original filename, date, temperature, number of scans and instrument and pulse program names. In addition, it makes the inspection of 2D and 3D experiments in progress very simple because the value of TD in the last dimension is extracted to provide the current experiment status. What you need to do: -------------------- Install the 5 scripts (drx2pipe, 1D2pipe, 2D2pipe, 3D2pipe and 4D2pipe) in a directory in your path and ensure that you have execute permissions on each one. The pulse program name is evaluated to determine if the data was recorded as Echo/Antiecho. I use the string "ea" in the pulse program name to flag this, and change yMODE to "Rance-Kay" in the convert.com script. I also use other pairs of letters to describe the experiment. These pairs are stripped off the pulse program name in order to make a guess at the output filename e.g. hnco.fid. You will need to edit these pairs according to your own naming convention. Edit drx2pipe to set the directory name for the nD2pipe scripts - these lines are marked in drx2pipe. Also edit it for allowed instrument names ("spect" is not an allowed name, I use an alias such as "drx500", so the string "drx" is checked for). If you wish to add a comment to the conversion file header simply add the string "; NMRPipe" followed by the text to appear in the header wherever you add comments in your pulse program. Each occurrence of this string is replaced by "#" in the file convert.com so it is treated as a comment. I use this feature to remind users of the phasing in the indirect dimensions, but it could also be used for example to state the sign of particular peaks in the data. The mixing time for NOESY data can be reported in the convert.com header. Just add the line ";Pipeinfo NOESY" in the comments section of your pulse program, and the value of d9 will be reported in ms. If you use a delay other than d9 for NOESY mixing times, edit drx2pipe where indicated. For those who use 4D NMR the script 4D2pipe makes assumptions about the way the data has been acquired. This is essential because XWIN-NMR currently does not handle 4D NMR experiments in eda. The A dimension nucleus label is stored in the parameter EXP, the incremented delay is D20 and the number of complex points is set by L20. The carrier is derived from the nucleus label. If you run 4D experiments differently from this you will need to change 4D2pipe accordingly. It has been written for SGI's running Irix 5.3-6.5. No guarantee whatsoever is provided. No attempt has been made to make the scripts applicable to the way every Bruker user runs their experiments. You are responsible for customizing them to suit your method of working and your own needs. Note that there is a bug in XWIN-NMR which means that the Z dimension SWH value in 3D experiments is sometimes incorrectly recorded. The value is therefore calculated from the parameter IN10, but this will fail if ND10 <> 2. How to run the scripts: ----------------------- Type "drx2pipe" and you will be asked to enter the pathname of the data on the spectrometer up to and including the EXPNO. The file convert.com is created and displayed, and you are asked if you want to convert the data now. If you answer "y" or hit return the data will be put into a directory called "fid" within your current directory. If you prefer to use a different output filename answer "e" and use your favorite editor (specified by setting the environment variable $EDITOR; vi is used if not set) to change the convert.com file. Here is an example of the output: #! /bin/csh -f # convert.com # Created by drx2pipe on Thu Apr 4 13:25:42 PST 1996 # Data recorded at 308.0K on drx500 # Thu Apr 4 12:10:51 1996 # File: /u/data/user/nmr/mydata/8/acqus # using pulse program hncoeags3d with 16 scans per FID # Phases = -90, 180 for both indirect dimensions, but P0 for 13C is approx. # bruk2pipe -in /u/data/user/nmr/mydata/8/ser -DMX -decim 24 -noswap \ -xN 1024 -yN 64 -zN 128 \ -xT 512 -yT 32 -zT 64 \ -xMODE Complex -yMODE Rance-Kay -zMODE Complex \ -xSW 8012.821 -ySW 1571.339 -zSW 1635.056 \ # -xSWppm 16.021 -ySWppm 31.006 -zSWppm 13.002 \ -xOBS 500.130000 -yOBS 50.677748 -zOBS 125.757453 \ -xCAR 4.702 -yCAR 119.000 -zCAR 176.000 \ -xLAB 1H -yLAB 15N -zLAB 13C \ -ndim 3 -aq2D States \ | pipe2xyz -out fid/hnco%03d.fid -verb -ov -nofs Reference: ---------- 1. "NMRPipe - A Multidimensional Spectral Processing System Based On Unix Pipes", F Delaglio et al, J Biomol NMR 6 #3, pp277-93 (1995). If you find any bugs or have suggestions for improvement please contact me. Good luck! Duncan M Smith Molecular Structure Department Mailstop 14-2-B Amgen Inc. One Amgen Center Drive Thousand Oaks CA 91320-1789 USA Phone (805) 447-3171 Fax (805) 499-7464 E-mail duncan@amgen.com