spectrum format for HNCACO

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

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Jun Yang

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Dec 17, 2021, 1:33:25 PM12/17/21

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Isn't HN(CA)CO for C'(i) only? Jun

Lee, Woonghee

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Dec 17, 2021, 1:47:12 PM12/17/21

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Jun, you can find the experiment profiles from here: http://i-pine.nmrfam.wisc.edu/files/nmr_experiment_profile.txt

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Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <pinenmr-u...@googlegroups.com> on behalf of "yangj...@gmail.com" <yangj...@gmail.com>

Date: Friday, December 17, 2021 at 11:33 AM
To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>

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Jun Yang

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Dec 17, 2021, 1:53:52 PM12/17/21

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Thanks. That's very helpful! Jun

Jun Yang

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Dec 17, 2021, 4:52:10 PM12/17/21

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Hi Woonghee,

I submitted a request for backbone assignment via the Pine-Sparky.2 automation window and got a submission success popup message. Will I also receive a submission email like the request for panderosa structure calculation because so far I haven't got anything?

Thanks.

Jun

Lee, Woonghee

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Dec 17, 2021, 5:04:07 PM12/17/21

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Hi Jun,

Have you checked the spam inbox? If you have the “token”, you can simply click “Web” button in the PINE-SPARKY.2 window.

Best,

Woonghee

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Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <pinenmr-u...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Friday, December 17, 2021 at 2:52 PM
To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>
Subject: Re: spectrum format for HNCACO

[External Email - Use Caution]

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Jun Yang

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Dec 17, 2021, 5:20:23 PM12/17/21

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I checked the "spam" folder and nothing related was there either. So I use the "I-Pine Web" button to submit the request online. This time I did receive the submission email almost right away, although with an error that I make a mistake to choose the wrong format. Should I re-submit everything all over again or can I just correct the wrong format and submit it again?

Thanks

Jun

Lee, Woonghee

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Dec 17, 2021, 5:22:40 PM12/17/21

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Jun, feel free to resubmit. You can also use a different email account.

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Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <pinenmr-u...@googlegroups.com> on behalf of "yangj...@gmail.com" <yangj...@gmail.com>
Date: Friday, December 17, 2021 at 3:20 PM
To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>
Subject: Re: spectrum format for HNCACO

I checked the "spam" folder and nothing related was there either. So I use the "I-Pine Web" button to submit the request online. This time I did receive the submission email almost right away, although with an error that I make a mistake to choose the wrong format. Should I re-submit everything all over again or can I just correct the wrong format and submit it again?

Thanks

Jun

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Jun Yang

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Dec 17, 2021, 5:57:37 PM12/17/21

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Thanks. It turns out that I won't get a submission email, only the result email as I now got both results. Is it possible to start the sequence with its real index instead of 1? I used the "pokybuilder.seq" sequence file with following format, but it still ends with 1 as the beginning index.

GLY 124
ALA 125
MET 126
GLY 127
SER 128
PRO 129

...

Thanks.

Jun

Lee, Woonghee

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Dec 17, 2021, 6:00:47 PM12/17/21

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Jun,

I-PINE webserver does not send a notification email upon submission. Because it does not take that long like calculating a structure.

You should stick with 1. You can change later using renumbering tool “rn”.

Best,

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <pinenmr-u...@googlegroups.com> on behalf of "yangj...@gmail.com" <yangj...@gmail.com>
Date: Friday, December 17, 2021 at 3:57 PM
To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>
Subject: Re: spectrum format for HNCACO

Thanks. It turns out that I won't get a submission email, only the result email as I now got both results. Is it possible to start the sequence with its real index instead of 1? I used the "pokybuilder.seq" sequence file with following format, but it still ends with 1 as the beginning index.

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Jun Yang

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Dec 17, 2021, 6:04:36 PM12/17/21

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Thanks. I'll check it out later. Have a nice weekend! Jun

Jun Yang

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Dec 18, 2021, 4:12:45 PM12/18/21

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Hi Woonghee,

I received a second result email (as below) from the job I submitted via PINE-SPARKY.2 module in poky that provide a "v2" result of the same job key. What should I do with it?

Thanks

Jun

==================================================

From: Mani Project Account <ma...@nmrfam.wisc.edu>
Sent: Friday, December 17, 2021 6:06 PM
To: xxxxxxxxxxxxxxxxxxx
Subject: PINE 2.0 job successfully finished

::::::::::::::
/home/mani/webserver/PINE/upload/script/success_new.txt
::::::::::::::

* PINE 2.0 is outdated and we recommend using I-PINE web server.
* Please use this result only to cross-validate against I-PINE result.
* I-PINE web server can be found at http://i-pine.nmrfam.wisc.edu

Bahrami, A., Assadi, A., Markley, J. L. & Eghbalnia, H., Probabilistic
Interaction Network of Evidence Algorithm and its Application to Complete
Labeling of Peak lists from Protein NMR Spectroscopy, PLoS Comput Biol. 2009
Mar;5(3):e1000307.

Dear User,

At the end of this email, you will find a link to the chemical shift assignment of your protein, secondary structure prediction, and possible referencing error.
For more information about the interpretation of output files please check out
http://pine.nmrfam.wisc.edu/instruction.htm

Notice that PINE is a probabilistic approach with probabilistic output.
Although PINE offers variety of output formats, it is extremely important to
consider all of the choices and their probabilitites in the PINE table output
format (protein_backbone_assignment.txt and sidechain_table.txt). All other
formats merely report the maximum probability answer. Please consider using
PINE-SPARKY for verfication of PINE assignments
(http://pine.nmrfam.wisc.edu/PINE-SPARKY). The visualization package is
already pre-installed in NMRFAM-SPARKY from software download page
(http://pine.nmrfam.wisc.edu/download_packages.html).

Please contact NMRFAM software development team at ma...@nmrfam.wisc.edu if you have any question or comments about the assignment. We will appreciate if you send us feedbacks about the quality of the assignment.

We would really appreciate citation of PINE if you found the results useful. The
manuscript information has been provided in the beginning of the email.

Thank you,
NMRFAM Software Development Team

links to the assignment:

==================================================

Lee, Woonghee

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Dec 18, 2021, 4:14:24 PM12/18/21

to Jun Yang, I-PINE/PINE and ssPINE user group

You can just look over the results and compare with I-PINE. That is the older version.

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From: pinenmr-u...@googlegroups.com <pinenmr-u...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Sent: Saturday, December 18, 2021 2:12:45 PM

To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>
Subject: Re: spectrum format for HNCACO

[External Email - Use Caution]

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Jun Yang

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Dec 18, 2021, 4:21:36 PM12/18/21

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I see. What's the command to regenerate all the graphic results from the downloaded file? Jun

Lee, Woonghee

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Dec 18, 2021, 4:23:02 PM12/18/21

to Jun Yang, I-PINE/PINE and ssPINE user group

It is I-PINE exclusive. You should read the texts for PINE 2.

Get Outlook for iOS

From: pinenmr-u...@googlegroups.com <pinenmr-u...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>

Sent: Saturday, December 18, 2021 2:21:36 PM

To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>
Subject: Re: spectrum format for HNCACO

[External Email - Use Caution]I see. What's the command to regenerate all the graphic results from the downloaded file? Jun

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Jun Yang

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Dec 20, 2021, 9:24:24 AM12/20/21

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I know it's exclusive generated by I-PINE. What I want to know is whether it is possible to re-generate these graphs in poky after I downloaded the result to local computer. Also the procedures to explore the i-pine result on your tutorial video is for nmrfam-sparky and it's quite different from poky interface. Is that an updated version to explain how to use "pine assigner", "pine graph assigner", "assign the best by i-pine", "select all floating i-pine labels", etc?

Best,

Jun

Lee, Woonghee

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Dec 20, 2021, 10:32:50 AM12/20/21

to Jun Yang, I-PINE/PINE and ssPINE user group

Hi Jun,

"pine assigner", "pine graph assigner", "assign the best by i-pine", "select all floating i-pine labels" You can still use those. In the “Key” of the PINE-SPARKY.2 plugin, yon just add “_v2” and click “Check”. But it will overwrite your currently imported results, and I don’t know if that is the that you want to do. I would rather open text files in two web browser side-by-side and identify the differences.

Best,

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672