FAQ

What is POKY?

POKY is a software suite for multidimensional NMR spectroscopy and three-dimensional structure calculation of biomolecules. Dr. Woonghee Lee is the developer of NMRFAM-SPARKY, PONDEROSA-C/S, PACSY, I-PINE, and more. Now, he develops the POKY suite with his team members, which is the ultimate integrated software platform embracing the enhanced versions of those popular software packages.

Why is POKY so innovative?

POKY is not only a significant advance in the research platform, but also a new software platform for convenient technology development. Its new extensible and scalable features by scripting and batching will enable users to freely use the offered automated analysis templates and build their own library sets to keep up with the rapid pace of technology. 

How can I cite POKY in my paper?

This is the paper for the citation. https://doi.org/10.1093/bioinformatics/btab180

How much does POKY cost?

POKY is free for academic users from non-commercial institutions. However, results from POKY must be published in public domains like wwPDB, BMRB and journals with the proper citation to POKY (https://doi.org/10.1093/bioinformatics/btab180). Please contact cuinnovations@ucdenver.edu for non-academic licenses. Reference POKY software or CU5598D in your email.

How can I activate my license key?

You can activate your license key from Poky -> File -> Licensing. If you are an academic user, click Use Academic License and Apply. Otherwise, get your license key (read above), put the key in the license key box, and click Apply. The license will be activated in the next run of Poky. Watch this tutorial video [click].

What is the minimum requirement to run POKY?

Three major operating systems are supported: Mac, Windows and Linux. POKY is compiled on Mac OS Catalina, Windows 10 and Ubuntu 20.04. We have confirmed that the Mac version supports Mojave and Big Sur as well. It has been reported that Apple Silicon Macs can also run Poky.

I don't have any NMR data. How can I start learning POKY?

POKY has SIM-PRAC, a program creating a protein NMR practice set. You can find it from Ext. menu -> Spectrum -> SIM-PRAC or type "me". You can follow many video clips from https://www.youtube.com/c/LeeGroupatCUDenver with the created practice set. 

How can I add a Python module that does not come with the Poky package?

There are two approaches. 

1. Open POKY Notepad (two-letter-code Pn). In the menu, select File -> Install PIP Python Module and type the package name.

2. If you wish to implement the automatic installation in the code, you can write the following two lines.

   •  from pyutil install module_install

   • module_install('module name')

Can POKY handle a spectrum file larger than 2GB?

Yes. Poky is native 64 bits software and able to handle large files even on Windows.

I have many SPARKY projects. Can I use them as they are?

Yes. They are 100% compatible. You can just set your working directory (File -> Set work directory) to the folder where your SPARKY projects are placed in.

How can I check whether my structure calculation job has submitted properly?

The job submitted mail will be sent to your inbox within a few minutes right after the submission. When there is any problem in the submission, you will get an error mail soon.

How long it would take for each calculation option?

The running time depends on the size of data and is variable in various situations. However, for the calculation of a small protein (about 9 KD), user may expect:

• roughly 3 hours for AUDANA/AUDASA automation

• roughly 3 hours for (ss)PONDEROSA-X refinement

• roughly 30 minutes for Constraints-only X

• roughly 2 hours for Final step

What is the difference between "implicit" and "explicit" water refinements in the Final step?

Implicit water refinement uses a force field called EEFX2 (Effective Energy Function for Xplor-NIH 2) that runs simulated annealing and water solvation simultaneously and gets 20 lowest energy models.

Explicit water refinement uses 20 lowest energy structures calculated within a vacuum box as precursors for the water solvation. It is a more conventional method that puts the pre-calculated structures into a water box (TIP3P) and runs energy minimizations.

How can I know my structure is reasonable?

Generally, one can say the structure is reasonable if it satisfies the followings:

• Number of long-range NOEs = about 5 times of the number of residues

• MP score < 2.5 (similar to the resolution in X-ray crystallography)

• MP outlier: close to 0 (zero)

• Number of violations: close to 0

• Dihedral angle deviations in the residue analysis: close to 0 for residues in rigid regions

• RDC deviations: close to 0 (green color in the RDC plot)

• R Corr value of the RDC plot: close to 1 (one)

How can I find detailed statistics for potential terms and violations?

See Calculation Reports (right-click the statistics table in the Poky Analyzer window and find Show Calculation Reports).

Alternatively, see the  final_xplor_each_##.pdb.stats file in the /BestEvaluated/XplorCalc folder in your job result. Users may drag-and-drop the file to Poky Notepad to view this file. 

What computing resources are used for the structure calculation?

POKY offers three options: NMRFAM servers, POKY servers, and your local computer. Currently, POKY servers are only viable option. It will automatically distribute jobs to integrated servers to POKY.

I am a Mac user and I see the error message saying "Incompatible library version: poky requires version 11.0.0 or later, but libX11.6.dylib provides version 10.0.0."

Your XQuartz is outdated. Please update it. XQuartz can be obtained from https://xquartz.org.

It is my first run, and POKY is very slow.

It is normal. Your computer is trying to understand/compile POKY. After this process in the first run, POKY will be fast.

Does POKY support 1D NMR?

Yes! You can open or drag'n drop an .ft1, 1r or .jdx/.dx file into the main window of POKY. 1D data will be created as "1D band". You can make assignments and work with other n-D data. w2 (horizontal) will be the dimension that you will use, w1 (vertical) will be an arbitrary dimension.

Can I process the data (time-domain to frequency-domain) with POKY?

Yes! You will see Processing under Ext. menu. You have access to POKY Phaser and easy-to-use POKY Notepad together for processing your data.

My POKY does not save a file. Why is that?

Make sure your license is activated. Otherwise, check your folder is writable.

I am a Mac user, and I do not see files in the file dialog.

You need to grant "Full Disk Access" to POKY from Security/Privacy in System Preferences.