NMR POKY/SPARKY USER GROUP - Google Groups

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This group is opened to announce news and discuss QnAs for POKY (new) and SPARKY (outdated) users. POKY from Woonghee Lee's group is available from https://poky.clas.ucdenver.edu. POKY is the modern software suite provides automated and visualized tools for multinuclear NMR data analysis including peak analysis, resonance assignment, titration and dynamics studies, 3D structure calculation, etc. The full manual is available at https://poky.clas.ucdenver.edu/poky_releases/manual/ — please check the manual and confirm if your problem also exists in the latest version of POKY before asking. You can use POKY in NMRbox as well (just type "poky"). Cite https://doi.org/10.1093/bioinformatics/btab180 for POKY (new) and https://doi.org/10.1093/bioinformatics/btu830 for NMRFAM-SPARKY (outdated).

Tom Goddard from UCSF Ferrin Lab. archived past message from Yahoo Groups: https://www.cgl.ucsf.edu/home/sparky/yahoo/msg_index.html

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Jul 16

POKY Manual is Now Online

Hi everyone, We're happy to announce that the POKY manual is now available as a web version,

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POKY Manual is Now Online

Hi everyone, We're happy to announce that the POKY manual is now available as a web version,

Jul 16

Asha Sanjeewani, Lee, Woonghee2

Jul 10

How to globally adjust spectrum referencing for relaxation/CPMG datasets?

Hi, In the POKY Notepad, File -> POKY Script -> Find additional …. Filter by “position”, and

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How to globally adjust spectrum referencing for relaxation/CPMG datasets?

Hi, In the POKY Notepad, File -> POKY Script -> Find additional …. Filter by “position”, and

Jul 10

Abhishek Bastiray, Lee, Woonghee2

Jul 3

Re: Loading the XEASY/Cyana peaklist in Poky

Hi, Do you mean “cy” ? Regarding the sequence file, please make sure you have this style. MET 1 THR 2

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Re: Loading the XEASY/Cyana peaklist in Poky

Hi, Do you mean “cy” ? Regarding the sequence file, please make sure you have this style. MET 1 THR 2

Jul 3

Sakshi Bhagat, Lee, Woonghee2

Jun 22

Please go “Ext.” menu, then “Selection”. You can click from there. Woonghee Lee, IEIP, MS, Ph.D.

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Please go “Ext.” menu, then “Selection”. You can click from there. Woonghee Lee, IEIP, MS, Ph.D.

Jun 22

pothula purushotham reddy, Lee, Woonghee2

Jun 10

unable pick the cross peak

Hi, When using “kr” for 3D-NOESY or TOCSY, leave the tolerance blank for any axis that should not be

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unable pick the cross peak

Hi, When using “kr” for 3D-NOESY or TOCSY, leave the tolerance blank for any axis that should not be

Jun 10

Mauricio Lasagna Arias, Lee, Woonghee3

Jun 8

Academic License

Thanks Dr. Lee, I found it. Mauricio Lasagna Mauricio D. Lasagna, PhD Associate Research Scientist

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Academic License

Thanks Dr. Lee, I found it. Mauricio Lasagna Mauricio D. Lasagna, PhD Associate Research Scientist

Jun 8

Jun 8

Re: [NMR POKY/SPARKY] BMRB를 이용한 2D 15N-HSQC assignment 문의드립니다.

Hi, Some deviations are expected because your protein construct is different and the environment is

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Re: [NMR POKY/SPARKY] BMRB를 이용한 2D 15N-HSQC assignment 문의드립니다.

Hi, Some deviations are expected because your protein construct is different and the environment is

Jun 8

Abhishek Bastiray, Lee, Woonghee3

Jun 4

Re: Error while using TALOS in Poky

Hi Prof. Lee, Yes my resonance list "rl" was the issue. I fixed it and it works now. Thank

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Re: Error while using TALOS in Poky

Hi Prof. Lee, Yes my resonance list "rl" was the issue. I fixed it and it works now. Thank

Jun 4

박소희, Lee, Woonghee2

Jun 1

Question about 4D spectrum analysis in POKY

Hi, Yes, it can open ucsf directly. 4rrrr, ft4, etc can be converted to ucsf. Experiment type should

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Question about 4D spectrum analysis in POKY

Hi, Yes, it can open ucsf directly. 4rrrr, ft4, etc can be converted to ucsf. Experiment type should

Jun 1

Maddilynn Mutchler, Lee, Woonghee2

May 28

Academic license issue

Hi, I don't think that is the problem. Please ensure you follow these steps. Download poky_win.

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Academic license issue

Hi, I don't think that is the problem. Please ensure you follow these steps. Download poky_win.

May 28

Abhishek Bastiray, Lee, Woonghee4

May 19

Re: transferring assignment from between spectra in Poky

If you are selecting a peak when you run “ta”, it only generates for that selected residue. Ensure

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Re: transferring assignment from between spectra in Poky

If you are selecting a peak when you run “ta”, it only generates for that selected residue. Ensure

May 19

Riley Carter, Lee, Woonghee3

Apr 23

Macrocylic peptide solution structure

Dr. Lee, Thank you for the clarification and help. Yours, Riley On Thursday, April 23, 2026 at 11:44:

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Macrocylic peptide solution structure

Dr. Lee, Thank you for the clarification and help. Yours, Riley On Thursday, April 23, 2026 at 11:44:

Apr 23

Asha Sanjeewani, Lee, Woonghee2

Apr 9

How to add HCCH-TOCSY and aromatic side chain spectra to the strip

Hi, HCCH-TOCSY is “HC” based. If you want to use it, you can have additional strip plot using “SP” or

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How to add HCCH-TOCSY and aromatic side chain spectra to the strip

Hi, HCCH-TOCSY is “HC” based. If you want to use it, you can have additional strip plot using “SP” or

Apr 9

Ning Zhang, Lee, Woonghee2

Apr 9

how to export chemical shift assignments in CYANA format

Hi, “xe” Woonghee Lee, IEIP, MS, Ph.D. Assistant Professor & Data Science and Chemistry

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how to export chemical shift assignments in CYANA format

Hi, “xe” Woonghee Lee, IEIP, MS, Ph.D. Assistant Professor & Data Science and Chemistry

Apr 9

Asha Sanjeewani, Lee, Woonghee5

Apr 2

Problem with Poky application through NMRbox

I changed .save10 to .save using the text editor, and it worked. Thank you so much, Dr. Lee. On Wed,

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Problem with Poky application through NMRbox

I changed .save10 to .save using the text editor, and it worked. Thank you so much, Dr. Lee. On Wed,

Apr 2

Korey R, Lee, Woonghee2

Mar 12

Assignment chemical shift precision

Open the python console “py”, and run this. print('\n'.join([f"{p.assignment}\t" +

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Assignment chemical shift precision

Open the python console “py”, and run this. print('\n'.join([f"{p.assignment}\t" +

Mar 12

Karla Martinez Pomier, Lee, Woonghee2

Feb 25

Cannot display CHESCA matrix and results on Poky

Hi, When using iCloud, data access permission can be an issue. Probably, you can just try to change

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Cannot display CHESCA matrix and results on Poky

Hi, When using iCloud, data access permission can be an issue. Probably, you can just try to change

Feb 25

Abhishek Bastiray, Lee, Woonghee3

Feb 16

Re: Can not generate NMRSTAR file in Poky

Prof. Lee, Thank you so much. I had a significant number of unused assignments. I can generate the

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Re: Can not generate NMRSTAR file in Poky

Prof. Lee, Thank you so much. I had a significant number of unused assignments. I can generate the

Feb 16

Korey R, Lee, Woonghee2

Feb 11

creating strip plots from hNcacoNNH

Hi, Simply "sp" and set up spectra from menu. Then add strips. based on peaks. It may be

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creating strip plots from hNcacoNNH

Hi, Simply "sp" and set up spectra from menu. Then add strips. based on peaks. It may be

Feb 11

Tanveer Shaikh, Lee, Woonghee4

Feb 11

Issue in vS slices sfter peak integration

Hi, Black line is from raw data, and it looks flat in your screenshot, while contours are drawn. This

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Issue in vS slices sfter peak integration

Hi, Black line is from raw data, and it looks flat in your screenshot, while contours are drawn. This

Feb 11

Tanveer Shaikh, Lee, Woonghee2

Feb 9

Issue with pi command

Hi, Please use “it” peak integration option. Best, Woonghee Lee, IEIP, MS, Ph.D. Assistant Professor

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Issue with pi command

Hi, Please use “it” peak integration option. Best, Woonghee Lee, IEIP, MS, Ph.D. Assistant Professor

Feb 9

Thinh Bui, Lee, Woonghee2

Jan 26

POKY for Non-Ribosomal Cyclic Peptide 3D-Structure Calculation

Hi, Certainly, you can use POKY for that by hybrid approach combining automation tools and manual

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POKY for Non-Ribosomal Cyclic Peptide 3D-Structure Calculation

Hi, Certainly, you can use POKY for that by hybrid approach combining automation tools and manual

Jan 26

Jan 13

Re: [NMR POKY/SPARKY] Issues with POKY Opening

It varies. But not too long. Less than a minute in general, and it should be instant after that.

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Re: [NMR POKY/SPARKY] Issues with POKY Opening

It varies. But not too long. Less than a minute in general, and it should be instant after that.

Jan 13

Molly Weber, Lee, Woonghee2

Jan 12

Installation on Mac

That's your password. Woonghee Lee, IEIP, MS, Ph.D. Assistant Professor & Data Science and

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Installation on Mac

That's your password. Woonghee Lee, IEIP, MS, Ph.D. Assistant Professor & Data Science and

Jan 12

pothula purushotham reddy, Lee, Woonghee2

Jan 11

Hi, CHESCA-I compares CHESCA-CL results for N and H individually. To mimic this, vary the N-to-H

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Hi, CHESCA-I compares CHESCA-CL results for N and H individually. To mimic this, vary the N-to-H

Jan 11

Abhishek Bastiray, Lee, Woonghee3

Jan 9

Re: Issues with XEASY file format in Poky

Thank you Prof. Lee. It worked, I was able to remove the lines using the above mentioned script.

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Re: Issues with XEASY file format in Poky

Thank you Prof. Lee. It worked, I was able to remove the lines using the above mentioned script.

Jan 9

12/11/25

Re: unable to generate .tab file POCY

Hi, You need to use “ce”. That will generate a file for CS-Rosetta. It will ask the “condition” to

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Re: unable to generate .tab file POCY

Hi, You need to use “ce”. That will generate a file for CS-Rosetta. It will ask the “condition” to

12/11/25

pothula purushotham reddy, Lee, Woonghee2

12/7/25

reference for CHESCA and CHESPA

Hi, If your alignment between spectra is good, you will be still good to go. Best, Woonghee Lee, IEIP

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reference for CHESCA and CHESPA

Hi, If your alignment between spectra is good, you will be still good to go. Best, Woonghee Lee, IEIP

12/7/25

12/1/25

Re: POKY perturbation analysis query

Hi, If you want to use linewidths, you have to fit/integrate peaks (“pi”) first. FWHM won't be

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Re: POKY perturbation analysis query

Hi, If you want to use linewidths, you have to fit/integrate peaks (“pi”) first. FWHM won't be

12/1/25

Tanveer Shaikh, Lee, Woonghee3

11/20/25

Assignment labels for 3d experiments

Thank you Dr. Lee, So, the correct format should be K10N-G9CA-K10H. Also, sorry about using the wrong

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Assignment labels for 3d experiments

Thank you Dr. Lee, So, the correct format should be K10N-G9CA-K10H. Also, sorry about using the wrong

11/20/25

Ning Zhang, Lee, Woonghee4

11/11/25

T1/T2 processing error

Oh, arbitrary assignments are fine (like Z1H-N as you did). First time point assignment labels on

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T1/T2 processing error

Oh, arbitrary assignments are fine (like Z1H-N as you did). First time point assignment labels on

11/11/25

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