Dear all,

I just uploaded a new version of NMRFAM-Sparky (BUILD 11/01/2018), and it has been a few months since I uploaded previous one so I briefly note here what has been done.

- I found user interests in using ucsfdata handy so I uploaded a new version of NMRFAM-Sparky that includes the easy_ucsfdata helper program (two-letter-code Du).

- Also, this version has a fix that creates view section if the section disappeared which would result in neither allowing to access by a user nor displaying a spectral view for the spectrum. It has been advised to make a new save file and copy view and paste to the old save file but this is not necessary anymore.

- Predict-and-confirm method implementation (two-letter-code ta) for 4 aromatic experiments. If you have CB assignments, it is just move a simulated assigned peak to a signal and type cu to detach a _s tag.

- Now, the automated assignment system, the I-PINE, supports 29 experiments including some 4D data. I have updated the PINE-SPARKY.2 (two-letter-code ep) accordingly. http://i-pine.nmrfam.wisc.edu

- Automated peak picker APES (two-letter-code ae) asks if a user wants to run an automated assignment by I-PINE (two-letter-code ep). And the I-PINE runs the automated structure calculation (two-letter-code c3) if NOESY data exist by using PONDEROSA-C/S with AUDANA algorithm, so it goes full automation without any supervision by a human. The AUDANA uses the Xplor-NIH for simulated annealing with its own NOE assignment algorithm assisted by the PACSY DB.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921114/

- A user can manually intervene at any step to improve the results while full automation from scratch is not giving you perfect assignments and structures anyways. For instance, you just run APES and you can pick more peaks and delete noise peaks while you wait for I-PINE results. Sometimes, the intermediate results from the next step help to improve the current step. This iterative employment of automation and a little bit of touch will be very efficient.

- PONDEROSA plugin (two-letter-code c3) has been improved as well. It will accept disulfide bonds, blacklist and whitelist so that a user does not need to run Ponderosa Client separate in case they want to use these information when using just AUDANA algorithm. If you want to know about blacklist and whitelist, please refer figure 14 in this paper:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861749/

- Some of you may be already noticed that the I-PINE provides a URL link to a web report page that visualizes assignment quality, structures, hydrophobicity, an HSQC spectrum, phi/psi angles, RCI-S2 (thanks to TALOS-N), etc. Organized individual outputs will be also listed at the left-bottom section.

I hope you enjoy it.

Best,

Woonghee