Re: PINE Question

[Lee, Woonghee]

Hi Chris,

LACS tells you the offset. You can apply that in "st" windows.

Best,

Woonghee

Get Outlook for iOS

---

From: Christopher Zerio <ze...@pharmacy.arizona.edu>
Sent: Tuesday, March 2, 2021 12:27:30 PM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Subject: Re: PINE Question

 

Woonghee,

Thank you so much for your help. I was able to fix the problem and successfully run PINE. I have one other quick question. My NMR data were collected on a Bruker spectrometer, and I used NMRFAM-Sparky to process the data. The scientist who runs our NMR facility mentioned something about a 2.7 ppm shift in the data when using Bruker spectrometers. Is there a way to correct for this in NMRFAM-Sparky? I am assuming that this shift needs to be corrected for before the NMR data are submitted to the BMRB. I really appreciate your help.

Thanks again,

Chris Zerio

---

From: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Sent: Sunday, February 28, 2021 7:35 PM
To: Christopher Zerio <ze...@pharmacy.arizona.edu>
Subject: Re: PINE Question

 

I advise you updating the program. Is it the latest version? Also, make sure your assignment format is valid one like M1CA.

Get Outlook for iOS

---

From: Christopher Zerio <ze...@pharmacy.arizona.edu>
Sent: Sunday, February 28, 2021 7:26:23 PM
To: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Subject: Re: PINE Question

 

Hi Woonghee,

Thanks for the quick reply. I think the problem is I can't perform "rn", and I'm not sure why. When I try to use rn, I get an error:

Exception in Tkinter callback

Traceback (most recent call last):

  File "/Applications/nmrfam-sparky-mac/NMRFAM-SPARKY.app/Contents/Resources/python/lib-tk/Tkinter.py", line 1345, in __call__

    return self.func(*args)

  File "/Applications/nmrfam-sparky-mac/NMRFAM-SPARKY.app/Contents/Resources/python/sparky/myseq.py", line 288, in okay_cb

    for tAssign in pAssign:  # (M1, CA)

TypeError: 'NoneType' object is not iterable

It also appears that "rn" is changing the numbering of one of my spectra, but not all of them. Is there an obvious fix to this?

Thank you again for your help,

Chris Zerio

---

From: Lee, Woonghee <WOONGH...@UCDENVER.EDU>
Sent: Saturday, February 27, 2021 4:50 PM
To: Christopher Zerio <ze...@pharmacy.arizona.edu>
Cc: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com>
Subject: Re: PINE Question

 

Dear Chris,

 

When you change your residue numbers by “rn”, you need to understand the logic. It will renumber all the existing peaks in your project, and overwrite [your project].proj.seq file. After using “rn”, quickly “dr” needs to be typed remove all resonances without corresponding peaks (basically “0” assignment you see in “rl” window). Then , you will need to check that overwritten .proj.seq file by using a text editor if that has been changed successfully.

 

Going back your native numbers can be done exactly same way. However, I usually stick with “1” as the starting number until the deposition because “1” is a lot easier using all different tools and only need to change once when I am ready.

 

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

woongh...@ucdenver.edu

 

https://sites.google.com/view/wlee-group

https://poky.clas.ucdenver.edu

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

 

 

 

 

From: Christopher Zerio <ze...@pharmacy.arizona.edu>
Date: Saturday, February 27, 2021 at 3:26 PM
To: Woonghee Lee <wh...@nmrfam.wisc.edu>
Subject: PINE Question

 

Hi Woonghee,

 

My name is Chris Zerio, and I am a PhD candidate in Pharmaceutical Sciences at the University of Arizona. I attended the NMRFAM Structure Determination Workshop in 2019. Recently, I was able to use the tools from the workshop to fully assign the backbone of a 13 kDa section of protein I am working with in NMRFAM-SPARKY. This was very exciting for me, and I really appreciate your help during the workshop!

 

I am writing to ask a question about PINE. I would like to run PINE in NMRFAM-SPARKY using the spectra I assigned (15N-HSQC, HNCACB, CBCACONH, HNCA, HNCOCA). However, I did all my assignments using the amino acid numbering from the protein (residues 24-144). So, my assignments are labeled 24-144, and not 1-120. When I go to submit the job to PINE, PINE will not accept my sequence file, because it says my assignment numbers don't match my sequence file numbers. I have tried the "sq" command to type my sequence, I have tried uploading .txt and .seq files, and I have tried manipulating the first residue with the "rn" command, but I have not been able to solve this.

 

Do you have any thoughts on how I can get a correct sequence file from resides 24-144 without having to manually go back and renumber my assignments from 1-120 so I can run PINE using my pre-assignment? I really appreciate the help.

 

Thanks,

Chris Zerio

 

Christopher J. Zerio

PhD Candidate - Pharmaceutical Sciences

Chapman Lab

University of Arizona