nmrview2-mac-linux

nmrview2-mac-linux - NMR Assignments using NMRView II:...

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NMR Assignments using NMRView II: Sequential Assignments DO THE FOLLOWING, IF YOU HAVE NOT ALREADY DONE SO: Check 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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Getting Started / Review The window below is for Mac OS X -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) -in the “main NMRView” menu , select File , then Read Star File . A new window will appear called “ReadNMRView Star File” window . In this window, in the nmrview directory, select the star file (database) called MYDatabase5.str and then click Open -another new window will appear. Close this window. NOTE: For Mac computers, in the rest of the tutorial, commands using the RIGHT mouse button may not work. Instead, use the left mouse button while holding down the command (apple) key. -in the “NMRView Console” window , type cd nmrview (return) source hsqc.tcl (return), then seqass (return), then source jump.tcl (return) -4 new windows should appear: “hsqc” , “hnco” , “hncacb” , and “cbcaconh” -put the cursor in the “cbcaconh” window. Right click to get the “Attributes” menu , then click on Attributes to get the “.specAttr” menu . Put the cursor in the “cbcaconh” window and use the up arrow ( ± ) on the keyboard to scroll through the planes ( 15 N) of the cbcaconh spectrum. You can monitor the 15 N chemical shift of the plane by looking at “ Z ” in the “.specAttr” window . Change “ Z ” to 118.74. -using the down Lvl arrow on the “.specAttr” window , change the contour level (remember to click Draw to see the changes) so that you can see the data (peaks) -in the “main NMRView” menu , select Assign then Peaks then List then cbcaconh . Scroll through the list to peak 10. Do the chemical shifts in the list correspond to those shown in the spectrum? -you can put the cursor in the
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nmrview2-mac-linux - NMR Assignments using NMRView II:...

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