Smartnotebook Example 1: hsqc-basic

---

	> cd snb-v5.0.6-examples1
	> cd hsqc-basic
	> snbview 

Next type "smartnotebook" in the nmrview console window (or "snb" for short).

	> snb

Great, let's see how we can go about making and assigning chains.

1. Click on the leftmost peak in the hsqc spectral display. A set of black cursors appears over the peak. On the smartnotebook main window, click on the "Spectra" button. You should see that we have selected Reference Id 0. Note: For MacOSX you may have to click twice on the button, the first click just activates the window. Fig 1
2. Click on the first connection in connections panel listing which is "4-0". The whole line is hilighted. Click "Display spectra" to display and verify that the connectivity is good. Fig 2
3. Click "Add to Chain". You now see 2 possible places in the sequence where this 2 residue chain can be assigned. Fig 3
4. In the Current Chain panel, click on the word "Start". We are going to add a connectivity to the start of the current chain.
5. There are 5 connectivities that can be appended to the start of the current chain. Click on the "74-4" entry, then click "Display Spectra". Fig 4
6. (optional) Click on a different connectivity (eg 90-4) and hit "display spectra" to confirm that this choice is not the correct one. Fig 5 Click the "74-4" entry again.
7. Click "Add to Chain". The assignment is now unambiguous. Fig 6
8. Select the "Best Fit" button. This allows us to verify how each chemical shift associated with current chain fits the shift constraints inherit with our sequence. Fig 7
9. After confirming the fit of each chemical shift, hit the "Assign" button. You have made your first assignment using smartnotebook! The ppm.out and *.xpk files in your output directory are updated with the correct shift values. Fig 8
10. (Optional) If you wish to continue to build this chain, you must unassign it first. Click unassign in the "Best Fit" window.

    Now we start work on a second chain.

11. Go to the "Chains" menu and select "Start new chain". This time we enter 94 in the Reference ID field and press return. For now, assume that hsqc Id 94 is arbitrarily chosen by the user as an interesting starting point. Note: You can search for interesting starting points by clicking "Search". Fig 9
12. Click on "94-26" and hit "Display Spectra". Fig 10
13. Click "Add to Chain". You now see 9 possible places in the sequence where this 2 residue chain can be assigned. Fig 11
14. In the Current Chain panel, click on the word "End". We are going to add a connection to the end of the current chain. There is only one connection that can be appended to the end of the current chain. Click on the "26-6" entry. Fig 12
15. Click "Display spectra" to verify the connection and "Add to Chain". Fig 13
16. Now there are only 3 possible places to assign this chain. Click on the word "End" of the current chain panel. Select the 6-116 connection, click the "Display spectra" button and finally click the "Add to Chain" button. Fig 14
17. The assignment is now unambiguous, select the "Best Fit" button. Confirm the fit of each chemical shift. Fig 15
18. (Optional) Are you at all curious how this short chain fits other sections in your sequence? Try clicking E108 in your sequence panel which on first glance looks like another assignment possibility. Notice that three proposed shifts exceed the expected shifts threshold of 3.0 standard deviations. However, smartnotebook does not prevent you from making this assignment if that is what you want. Fig 16
19. (Optional) Are you interested in seeing how long you can build this chain? Great, first make sure your current chain is unassigned. Smartnotebook does not allow you to edit an assigned chain. Now your mission, if you decide to take it, is to find the correct chain from Prolene to Prolene! Don't worry if you can't get it, eventually you will want to learn what all those numbers in the connections panel mean.
20. This example demonstrates an interesting shift in assignment philosophy. It is not necessary to start at certain amino acids in the sequence, just start at a connection that looks 'right' and see where the chain takes you. Software which pre-builds chains for the user would be an asset in the smartnotebook suite.

    When you are finished playing, select the "Quit nmrview" menu item under File.

Smartnotebook Examples

This file last updated: