LACS format

[Joel Mackay]

I am having issues figuring out exactly what the file format is that I should be using to submit chemical shifts to LACS. I am using NMRFAM-SPARKY, outputting an XEASY format file and using STARCH on the BMRB site to create an NMR-STAR formatted file. However, such a file (even after I add a Mol_residues_sequence entry) fails – and the error message isn’t so helpful.

 

I have looked at this page: http://pine.nmrfam.wisc.edu/LACS/instruction.htm

 

But am puzzled because the format shown doesn’t seem to be fully correct. There are only three columns listed in the “_loop” section (and these column names aren’t options in the STARCH converter), whereas there are 8 columns in the chemical shift list shown. See below:

 

   loop_

   _Residue_seq_code

   _Residue_label

   _Chem_shift_ambiguity_code

   4    2   LYS  HG2   H    1.61  .  2

   5    2   LYS  HD2   H    1.40  .  2

I wonder if you could send me example files that work so that I can trouble shoot. I’ve attached a file I tried to use.

 

A secondary question is that when I try to run LACS from within NMRFAM-SPARKY, it also fails – and I think it’s failing because I’m not providing an appropriately formatted sequence file. I wonder if you could show me what the correct format for that file is please?

 

Thanks in advance,

Joel Mackay

[Lee, Woonghee]

Dear Joel,

 

If you are running LACS directly from NMRFAM-SPARKY (two-letter-code lv), you will need to provide the sequence in “sq” window or you will be asked if there’s a gap between your assignments. If you provide your correct sequence file, it will run without a problem. Another thing you can try is to have your sequence number starting from 1. If none of them works, you can try I-PINE with “use pre-assignment” option turned on and see the LACS results from the I-PINE web results.

 

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://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

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: <pinenmr-u...@googlegroups.com> on behalf of Joel Mackay <joelpet...@gmail.com>
Date: Saturday, July 10, 2021 at 12:12 AM
To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>
Subject: LACS format

 

[External Email - Use Caution]

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[Joel Mackay]

hi Woonghee

If I enter my sequence with 'sq', I am able to submit a job to LACS via 'lv'.

However, it returns the error:

An unknown error has occured during the process of your job in LACS. Please make sure the assignment file is in the correct format. 

I don't see any guidelines for the 'assignment file' though so am not sure what I need to correct.

I see there is a box in 'lv' that allows you to apply only to selected groups. What does this mean? How does one select groups to be included?

Will the presence of pseudo atoms cause problems?

I also have several partly assigned residues (e.g., Pa and Pb for two prolines I haven't assigned yet). Do I need to get rid of these for the process to work?

[I also tried I-PINE, but it came back saying that the hnca.list file was 'not in the standard format for HNCA']

Thanks
Joel

[Joel Mackay]

Also, if I try ARECA, I get:

Traceback (most recent call last):

  File "C:\nmrfam-sparky-win32\python\lib-tk\Tkinter.py", line 1489, in __call__

    return self.func(*args)

  File "C:\nmrfam-sparky-win32\python\sparky\ponderosa.py", line 249, in call_areca_cb

    self.stoppable_call(self.arecasubmit_cb)

  File "C:\nmrfam-sparky-win32\python\sparky\tkutil.py", line 1263, in stoppable_call

    result = apply(func, args)

  File "C:\nmrfam-sparky-win32\python\sparky\ponderosa.py", line 822, in arecasubmit_cb

    self.submission(1)

  File "C:\nmrfam-sparky-win32\python\sparky\ponderosa.py", line 650, in submission

    if abs(resonance1.group.number - resonance2.group.number) < 2: continue

TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'

as the error that comes back in NMRFAM-SPARKY. I don't know if this is useful?

Best regards
Joel

[Lee, Woonghee]

Hi Joel,

 

I see there is a box in 'lv' that allows you to apply only to selected groups. What does this mean? How does one select groups to be included?

 

It will check the residue numbers you are selecting in any spectra but if you select only small number of peaks it will fail as you might expect.

 

I also have several partly assigned residues (e.g., Pa and Pb for two prolines I haven't assigned yet). Do I need to get rid of these for the process to work?

 

Probably. Just remove assignments and make notes for the later and try again.

 

[I also tried I-PINE, but it came back saying that the hnca.list file was 'not in the standard format for HNCA']

 

Check your peak list if you have peaks CA range outside of 40-70ppm by accident.  

 

TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'

 

Some assignments are unrecognizeable. You check with “ca” and also in “rl” or “tb” windows.

 

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://poky.clas.ucdenver.edu

https://poky.clas.ucdenver.edu/wlee-group

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: <pinenmr-u...@googlegroups.com> on behalf of Joel Mackay <joelpet...@gmail.com>

Date: Sunday, July 11, 2021 at 2:43 AM
To: I-PINE/PINE and ssPINE user group <pinenmr-u...@googlegroups.com>

Subject: Re: LACS format

 

[External Email - Use Caution]hi Woonghee

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