nmrview1-mac-linux

nmrview1-mac-linux - NMR Assignments using NMRView I...

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NMR Assignments using NMRView I: Introduction to NMRView In your home directory, you should have a subdirectory called “nmrview”. The contents of that directory should be as shown below (subdirectories are followed by a / ): 8190.dba jump.tcl nmrview1-mac.pdf nvtcl/ pl198t.nv acc_c_average.pdb keys.tcl nmrview_2labs.tar pl181t.nv pl206t.nv hsqc.tcl MYDatabase5.str nmrview2-mac.pdf pl185t.nv THE FOLLOWING ARE VERY IMPORTANT! -in the file hsqc.tcl in the nmrview directory, there should be several (4 or 5) pointers to the nmrview subdirectory in your home directory. You need to change these to point to YOUR nmrview subdirectory in YOUR home directory. For instance, on the LINUX computers, this will be something like “/home/your-user-name/nmrview” where “your-user-name” is your user name. -do the same for the single (1) occurrence in the file MYDatabase5.str in the nmrview directory (the variable _Template_filename should be “/home/your-user-name/nmrview”) -finally, you should “cd” into your nmrview directory -you are now ready to begin
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Start the Program -start the program -on Mac computers, simply click on the NMRView icon in the Dock -on LINUX computers, open a terminal window, cd into your nmrview directory, and type “nv5” (no quotes, followed by return of course) You should see 3 windows/menus appear: 1). The first is the “Info” window , and says NMRView in big red letters. This window will disappear in a few seconds 2). The second is the “main NMRView” menu , and will appear at the top of your screen. -on Mac computers, this is as shown below -on LINUX, there will be a separate, movable window that appears at the top of the screen 3). The third is the “NMRView Console” window , and will appear at the bottom of your screen. You can enter commands in the console window command line. Help -in the “main NMRView” menu , choose Help , then User's Manual (Internal Viewer) -go ahead and browse through some of the options - you should find lots of information in the manual that will be of use to you later on as you become more familiar with the software -choose Close to exit the User's Manual
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Exercise 1: 2D 1 H, 15 N-HSQC The spectra of a short peptide (24 residues) bound to RNA will serve to demonstrate NMRView. The sequence of the peptide is: -2 –1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 g s M D A Q T R R R E R R A E K Q A Q W K A A N First, we will simply look at the 1 H, 15 N-HSQC spectrum, and get used to some of the features of NMRView. -in the “main NMRView” menu , choose Dataset , then Open Datasets . A new window will appear called “datasets” . Select the file named pl181t.nv (this file is in your nmrview directory), then click Open . -in the
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nmrview1-mac-linux - NMR Assignments using NMRView I...

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