PENCE / CIHR-Group Joint Software Centre

Funding for this software has been provided in part by the
Canadian Institutes of Health Research (CIHR Group)
and the
Protein Engineering Networks of Centres of Excellence (PENCE).

1. Latest News - Author's notes and comments for this and future versions
2. Bug report - Check here for the latest bug reports from our users.

3. Background - Copyright notice, References, User agreement, Acknowledgements, Project history
4. Release Notes - If you have used the previous version, here is a summary of the changes.

5. Introduction - Start here if you are a new user
6. Download and Installation
7. Start up and Examples - Learn and test the software

8. Smartnotebook in Detail
   1. Reference ID / Spectra Button - set the active reference ID number
   2. Search Button - Searching for interesting connectivities
   3. Connections Panel - Current connectivities list
   4. Current Chain Panel - Current chain of connectivities
   5. Sequence Panel - How the current chain and current assignments fit the sequence
   6. Buttons Panel - Commands for building/modifying chains
      • Display Spectra
      • Add to Chain
      • Delete Connection
      • Best Fit - assignment operations via the pop-up shift analysis window
   7. File Menu
   8. Options Menu
      • pipp_nav
      • Configure/Update
      • Folded Peaks
      • Create Connectivity
      • Spectra: Peak Labels
      • Spectra: Vertical Scale
   9. Chains Menu - chain selection
   10. Suggest Menu

9. File Summary - explanation of input/output files used
10. Advice in using the software on your own data

11. Advanced Topics
    • Missing Connections - Why did my chain stop?
    • Developer Notes - Software issues
    • Peakcon - Pattern recognition, finding connectivities
    • Troubleshooting and Questions
12. Appendix - How to pick your peaks in nmrview

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