BMRB (from CARA) to Sparky

Chathuri Savindya

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Jul 7, 2022, 11:54:29 AM7/7/22

to NMR POKY/SPARKY USER GROUP

Hi!

I found this video on how to import BMRB star files into Sparky:

I am using CARA, and I would like to do something similar to load my peaks into Sparky. I am aware of the LUA script that makes a sparky peak list, but I think the BMRB approach in the video is cleaner.

In CARA, I am using the "Write Assignments" script to create a BMRB file. However, when run Sparky's "Convert BMRB 3.1 to ... Sparky Resonance List (ns)" on this file, I get an empty file. There is nothing in the output "list" file to import.

I think the output file from CARA is probably missing some information that Sparky needs to convert, but I'm not sure. The beginning of my CARA file is at the end of this message. There is nothing before the first "loop_" line.

Any ideas?

Thanks,

Chathuri

--- snip ---

loop_
_Atom_shift_assign_ID
_Residue_author_seq_code
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code

1 2 2 GLN CA C 55.911 0.3 1
2 2 2 GLN CB C 30.423 0.3 1
3 2 2 GLN H H 8.199 0.020 1
4 2 2 GLN N N 120.003 0.3 1
5 3 3 TYR CA C 57.225 0.3 1
6 3 3 TYR CB C 43.235 0.3 1

Lee, Woonghee

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Jul 7, 2022, 12:01:23 PM7/7/22

to Chathuri Savindya, NMR POKY/SPARKY USER GROUP

Dear Chathuri,

That does not look like 3.1 version. That looks more like 2.1 version.

I am answering “HOW-TO” for POKY. Please see the group description.

You can just remove lines other than actual data, then use this script in POKY Notepad: https://github.com/pokynmr/POKY/blob/master/User_Modules/tab2poky_list.py

Then, you can simply read that in using that open icon in the UI, and propagate peaks with assignment labels using the “ta” tool.

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 (office), Rm 4128 (dry lab), Rm 4133 (wet lab)

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: <nmr-s...@googlegroups.com> on behalf of Chathuri Savindya <khcskari...@gmail.com>
Date: Thursday, July 7, 2022 at 9:54 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] BMRB (from CARA) to Sparky

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Chathuri Savindya

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Jul 7, 2022, 12:14:28 PM7/7/22

to NMR POKY/SPARKY USER GROUP

Thanks! I did find an updated Lua script that outputs a 3.1 BMRB format from CARA, but that's still producing a blank file when I use "ns" in Sparky (version 1.414/3.135). My adviser hasn't installed POKY on my linux system, but may try it on my own laptop. I'll also apply some pressure...

Anyway, here's the output from the BMRB 3.1 CARA Lua script.

Thanks again,

Chathuri

--- snip ---

loop_
_Atom_chem_shift.ID
_Atom_chem_shift.Entity_assembly_ID
_Atom_chem_shift.Comp_index_ID
_Atom_chem_shift.Comp_ID
_Atom_chem_shift.Atom_ID
_Atom_chem_shift.Atom_type
_Atom_chem_shift.Atom_isotope_number
_Atom_chem_shift.Val
_Atom_chem_shift.Val_err
_Atom_chem_shift.Assign_fig_of_merit
_Atom_chem_shift.Ambiguity_code
_Atom_chem_shift.Occupancy
_Atom_chem_shift.Details
#
# Ent. Comp Atom Assign. Atom
# Ass. indx Comp Atom Atom isot. Val fig.of Ambig.
# ID ID ID ID ID type num Val err merit code Occup Details
#________________________________________________________________________________
#
1 . 2 GLN CA C 13 55.911 0.3 . 1 . .
2 . 2 GLN CB C 13 30.423 0.3 . 1 . .
3 . 2 GLN H H 1 8.199 0.020 . 1 . .

Lee, Woonghee

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Jul 7, 2022, 12:23:32 PM7/7/22

to Chathuri Savindya, NMR POKY/SPARKY USER GROUP

“ns” won’t work because you don’t have sequence information in the file. The tab2poky_list script is more straightforward, flexible and easier. You can just use NMRbox, too. POKY is there. You just generate the resonance list file and copy to your computer.

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 (office), Rm 4128 (dry lab), Rm 4133 (wet lab)

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: <nmr-s...@googlegroups.com> on behalf of Chathuri Savindya <khcskari...@gmail.com>
Date: Thursday, July 7, 2022 at 10:14 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] BMRB (from CARA) to Sparky

[External Email - Use Caution]

Thanks! I did find an updated Lua script that outputs a 3.1 BMRB format from CARA, but that's still producing a blank file when I use "ns" in Sparky (version 1.414/3.135). My adviser hasn't installed POKY on my linux system, but may try it on my own laptop. I'll also apply some pressure...