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Automatic NMR assignment (I-PINE/ssPINE/RNA-PAIRS/MAGIC-ACT) user group

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Welcome.

This group is to communicate among I-PINE / ssPINE / RNA-PAIRS / MAGIC-ACT automatic assignment package users. The I-PINE is one of the most popular chemical shift assignment algorithms provided as a form of web server to the NMR community.

All available as user-friendly GUI plugins to the POKY suite (https://poky.clas.ucdenver.edu)

- I-PINE (two-letter-code "ep"): protein solution NMR

- ssPINE (two-letter-code "EP"): protein solid-state NMR

- RNA-PAIRS (two-letter-code "ER"): imino RNA solution NMR

- MAGIC-POKY (two-letter-code "MA"): methyl-labeled protein NMR

Woonghee Lee, Ph.D.

0 selected

Aug 21

Re: I-Pine question

Dear Garry, The “Pre-assignment” option still requires your data to align with your given assignments

unread,

Re: I-Pine question

Dear Garry, The “Pre-assignment” option still requires your data to align with your given assignments

Aug 21

Maia Sraga, Lee, Woonghee2

Aug 8

ssPINE Pre-Assignment

Maia, just one is enough. If the given assignment makes sense, it will be prioritized. However, if

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ssPINE Pre-Assignment

Maia, just one is enough. If the given assignment makes sense, it will be prioritized. However, if

Aug 8

Maia Sraga, Lee, Woonghee2

Aug 7

NCACA and NCOCO peaks for submission

Dear Maia, It is always better to do your best to remove incorrectly placed peaks and add peaks that

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NCACA and NCOCO peaks for submission

Dear Maia, It is always better to do your best to remove incorrectly placed peaks and add peaks that

Aug 7

Maia Sraga, Lee, Woonghee5

Jul 9

Unlabeled Histidines in Protein to be Assigned

Right, thank you! On Wednesday, July 9, 2025 at 2:19:46 PM UTC-4 Lee, Woonghee wrote: Both ways are

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Unlabeled Histidines in Protein to be Assigned

Right, thank you! On Wednesday, July 9, 2025 at 2:19:46 PM UTC-4 Lee, Woonghee wrote: Both ways are

Jul 9

yan zhang, Lee, Woonghee2

9/11/24

[I-PINE bug report]

Yan, please try I-PINE for POKY through "ep" plugin in POKY. -- Woonghee Lee, Ph.D.

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[I-PINE bug report]

Yan, please try I-PINE for POKY through "ep" plugin in POKY. -- Woonghee Lee, Ph.D.

9/11/24

yan zhang, Woonghee Lee2

7/12/24

Question for [I-PINE]

I-PINE for POKY works okay. Are you using "ep" in POKY? On Friday, July 12, 2024 at 1:29:27

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Question for [I-PINE]

I-PINE for POKY works okay. Are you using "ep" in POKY? On Friday, July 12, 2024 at 1:29:27

7/12/24

James Chen, Lee, Woonghee2

5/21/24

error submitting ssPINE job

Dear Bo, Two things you can check. First, the format should be, Assignments w1 w2 w3 Data Height . .

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error submitting ssPINE job

Dear Bo, Two things you can check. First, the format should be, Assignments w1 w2 w3 Data Height . .

5/21/24

Anthony Legrand, Lee, Woonghee2

3/20/24

Starting structure for PONDEROSA calculations

You can add pdb file as a restraint to assist NOE analysis. -- Woonghee Lee, Ph.D. Assistant

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Starting structure for PONDEROSA calculations

You can add pdb file as a restraint to assist NOE analysis. -- Woonghee Lee, Ph.D. Assistant

3/20/24

Anthony Legrand, Lee, Woonghee4

11/28/23

Repeated unknown error

Dear Anthony, Glad you have resolved. Yes, the file extension makes a difference. You have to let I-

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Repeated unknown error

Dear Anthony, Glad you have resolved. Yes, the file extension makes a difference. You have to let I-

11/28/23

gary thompson, Lee, Woonghee2

3/9/23

triple resonance test with sin system file

Gary, I haven't used the NMRFAM web server after the hacking by the online gambling site so I don

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triple resonance test with sin system file

Gary, I haven't used the NMRFAM web server after the hacking by the online gambling site so I don

3/9/23

Leonardo Garcia Dettori, Lee, Woonghee2

3/1/23

N15 N15 - NOESY

Leo, No, I-PINE supports only NHh and CHh data. You will need to use your data to verify assignments.

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N15 N15 - NOESY

Leo, No, I-PINE supports only NHh and CHh data. You will need to use your data to verify assignments.

3/1/23

Christopher Williams, Lee, Woonghee4

9/13/22

ssPine - Gap in Sequence

Actually, it is cumbersome. You should provide a sequence file starting from 1 for both jobs. ssPINE

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ssPine - Gap in Sequence

Actually, it is cumbersome. You should provide a sequence file starting from 1 for both jobs. ssPINE

9/13/22

Lee, Woonghee, CHAD RIENSTRA3

4/25/22

Current server issues

Thanks Chad. I hope it gets back soon while it affects a wide array of users. Woonghee Get Outlook

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Current server issues

Thanks Chad. I hope it gets back soon while it affects a wide array of users. Woonghee Get Outlook

4/25/22

은현종, Lee, Woonghee2

4/24/22

Is there a problem with PINE webserver?

Please use the latest version of POKY. NMRFAM has a server issue. The latest version of POKY uses

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Is there a problem with PINE webserver?

Please use the latest version of POKY. NMRFAM has a server issue. The latest version of POKY uses

4/24/22

Gabriele Coluccino, Lee, Woonghee4

4/20/22

Error HCCH-TOCSY Format

Gabriele, Still that is the error from your peaks. For H(C)CH-TOCSY, average H, C ppms must fall in 0

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Error HCCH-TOCSY Format

Gabriele, Still that is the error from your peaks. For H(C)CH-TOCSY, average H, C ppms must fall in 0

4/20/22

1/26/22

Re: PINE sequence input

Hi Robert, I think you can just add additional PROs between two chains. Try and let us all know if it

unread,

Re: PINE sequence input

Hi Robert, I think you can just add additional PROs between two chains. Try and let us all know if it

1/26/22

Jun Yang, Lee, Woonghee18

12/20/21

spectrum format for HNCACO

Hi Jun, "pine assigner", "pine graph assigner", "assign the best by i-pine

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spectrum format for HNCACO

Hi Jun, "pine assigner", "pine graph assigner", "assign the best by i-pine

12/20/21

Christopher Williams, Lee, Woonghee3

8/16/21

Pre-assignment File Error

Thank you very much, that seemed to be the issue. Just needed to make my pre-assignment appear to

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Pre-assignment File Error

Thank you very much, that seemed to be the issue. Just needed to make my pre-assignment appear to

8/16/21

Jennifer Zhao, Lee, Woonghee3

7/20/21

Error in PINE server submission

Thank you Woonghee, I'll try that. On Tuesday, July 20, 2021 at 3:08:52 PM UTC+10 Lee, Woonghee

unread,

Error in PINE server submission

Thank you Woonghee, I'll try that. On Tuesday, July 20, 2021 at 3:08:52 PM UTC+10 Lee, Woonghee

7/20/21

Joel Mackay, Lee, Woonghee5

7/11/21

Hi Joel, I see there is a box in 'lv' that allows you to apply only to selected groups. What

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Hi Joel, I see there is a box in 'lv' that allows you to apply only to selected groups. What

7/11/21

Wenyan Guan, I-PINE/PINE and ssPINE user group3

6/2/21

Oh, I see. Thank you very much, Woonghee! It works now. Thanks. Have a good night! Wenyan 在2021年6月1日

unread,

Oh, I see. Thank you very much, Woonghee! It works now. Thanks. Have a good night! Wenyan 在2021年6月1日

6/2/21

3/19/21

Hi Sichun, If you align a diagonal peak, you don't need to worry. Cheers, Woonghee -- Woonghee

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Hi Sichun, If you align a diagonal peak, you don't need to worry. Cheers, Woonghee -- Woonghee

3/19/21

Ivan S. Podkorytov, Lee, Woonghee2

3/15/21

I-PINE, CA and CO shifts

Hi Ivan, It is difficult to identify what is going on with your data unless I have access to the raw

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I-PINE, CA and CO shifts

Hi Ivan, It is difficult to identify what is going on with your data unless I have access to the raw

3/15/21

Ivan S. Podkorytov, Lee, Woonghee2

3/12/21

I-PINE, CO shifts

Dear Ivan, 1) The file protein_backbone_assignment.txt contains almost complete assignment with

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I-PINE, CO shifts

Dear Ivan, 1) The file protein_backbone_assignment.txt contains almost complete assignment with

3/12/21

kai xue, Lee, Woonghee2

3/9/21

Dimer assignment

Hi Kai, The message indicates the generated spin system matrix is too sparse to continue the

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Dimer assignment

Hi Kai, The message indicates the generated spin system matrix is too sparse to continue the

3/9/21

3/2/21

Re: PINE Question

Hi Chris, LACS tells you the offset. You can apply that in "st" windows. Best, Woonghee Get

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Re: PINE Question

Hi Chris, LACS tells you the offset. You can apply that in "st" windows. Best, Woonghee Get

3/2/21

Ivan S. Podkorytov, Lee, Woonghee4

2/4/21

Dear Ivan, I-PINE does not average chemical shifts. It changes chemical shifts to integer numbers and

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Dear Ivan, I-PINE does not average chemical shifts. It changes chemical shifts to integer numbers and

2/4/21

Lee, Woonghee, Sichun Yang4

2/3/21

Re: Pine graph assigner

Dear Sichun, They don't block. But if they look too crowded, you can hide/show them by “ls”. View

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Re: Pine graph assigner

Dear Sichun, They don't block. But if they look too crowded, you can hide/show them by “ls”. View

2/3/21

1/12/21

Re: [NMR-SPARKY] I-PINE selective labelling

Hi Chris, (H)CCONH-TOCSY is used in sidechain assignments. Ideally, it would have been nice if we

unread,

Re: [NMR-SPARKY] I-PINE selective labelling

Hi Chris, (H)CCONH-TOCSY is used in sidechain assignments. Ideally, it would have been nice if we

1/12/21

11/2/20

Re: Protein Sequence format I-PINE webserver

Dear Arun, If you are using NMRFAM-SPARKY, you can easily renumber by two-letter-code “rn”. I-PINE is

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Re: Protein Sequence format I-PINE webserver

Dear Arun, If you are using NMRFAM-SPARKY, you can easily renumber by two-letter-code “rn”. I-PINE is

11/2/20

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