Practical Advice for the Assignment Process using smartnotebook

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1. Make good use of the search window especially the Next/Prev buttons to find the starting point of my new chains. I am looking for connections that score high in comparison to the alternative choices.

   This is a bit of a paradigm shift because spectroscopists are used to the idea that you start chaining at a particular residue (eg, thr or ala). But the most effective use of smartnotebook starts with building unbiased, unambiguous chains no matter what your starting point. You will see that the assignment process takes care of itself. This leads into the next point.

2. Make and assign the easy chains first stopping whenever a choice is not clear cut. When I come back to these chains later, I sometimes find that the "Stat" field has resolved my ambiguity issues and only one obvious unassigned connection remains.

3. When the easy stuff is done, or when you feel lucky, select a chain which has a number of choices for an endpoint, continue the chain with your best guess. Perhaps you are able to extend the current chain several residues, this gives alot of evidence that you have made the right choice at this ambiguity. You will feel more confidence in your decision if you have already assigned easy stuff first.

4. Although the Missing Connections section is somewhat advanced, you will find it invaluable for how to tackle a difficult to assign region. You should also check the frequently updated bug report if you have not done so already.

5. Consider the possibility that you cannot assign the whole sequence completely with smartnotebook. Feel free to abandon smartnotebook and pick up your nicely formatted *.xpk files and ppm.out from the output directory snb.out. Use manual or other software to finish the work. Don't let the frustration of trying to assign those last 8 residues color the reality that you should have learned a whole bunch about your protein that you would not have known otherwise. Smartnotebook does not make a single assignment, you do, you are responsible for making the correct assignment choices.

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