Asurin Software Developer

NMR software and file formats

05 Apr 2023

Recently worked on helping my previous PI analyze some NMR (Nuclear Magnetic Resonance) data for some molecules. I am used to analyze NMR data with Sparky. I am going to discuss about some NMR related software and file formats in this post.

Short background

The raw data are usually obtained from Bruker NMR machines or Varian NMR machines. Varian was trying to produce 1 GHz NMR machine and failed. It went bankrupt and was bought by Agilent. The software from Bruker is called TopSpin. TopSpin is free for acedamic usage. The software from Varian is called Vnmrj. It was not free but now there is an open source version called OpenVnmrj.

UCSF format

ucsf format is the format used by Sparky and its successor Poky.

Conversion from bruker

The ucsf format could easily be converted from bruker format by using the following command:

bruk2ucsf.exe .\USF_BH_20230328_TOCSY\27\pdata\1\2rr usf_bh_20230328_tocsy.ucsf

bruk2ucsf.exe comes with sparky software distribution.

The raw date from Bruker will only have ser file. We have to use TopSpin to process the raw data to get the 2rr file.

Conversion from vnmrj

To get ucsf format from Vnmrj is a little more complicated. You have to have Vnmrj software installed in your system. The current OpenVnmrj can be installed on Ubuntu 20.04. After opening your data in OpenVnmrj, you have to run trace='f1' and flush in Vnmrj. Then run:

vnmr2ucsf exp7/procpar exp7/datdir/phasefile exp7.ucsf H H

to generate the ucsf file. The exp7 means you have opened your date in experiment7 in your Vnmrj softawre. The exp7 folder should be in ~/vnmrsys/data folder.

UCSF data format

Detailed information about the data format could be found here.

Let’s analyze the headers of a C13HSQC file:

00000000   55 43 53 46  20 4E 4D 52  00 00 02 01  00 02 ** **  ** ** ** 00  00 00 00 4D  6F 6E 20 41  UCSF NMR......*****....Mon A
0000001C   70 72 20 30  33 20 31 31  3A 33 32 3A  33 34 20 32  30 32 33 00  00 00 00 00  00 00 00 00  pr 03 11:32:34 2023.........
00000038   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
00000054   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
00000070   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 40 01 B4  00 00 00 00  .....................@......
0000008C   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
000000A8   00 00 00 00  00 00 00 00  00 00 00 00  31 33 43 00  00 00 00 00  00 00 04 00  00 00 04 00  ............13C.............
000000C4   00 00 00 80  42 FB 8B 64  46 A2 20 D8  42 96 03 2B  00 00 00 00  00 00 00 00  00 00 00 00  ....B..dF. .B..+............
000000E0   80 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
000000FC   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
00000118   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
00000134   31 48 00 00  00 00 00 00  00 00 04 00  00 00 04 00  00 00 00 80  43 FA 13 85  45 DF 36 DB  1H..................C...E.6.
00000150   40 A0 00 40  00 00 00 00  00 00 00 00  00 00 00 00  80 00 00 00  00 00 00 00  00 00 00 00  @..@........................
0000016C   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
00000188   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  ............................
000001A4   00 00 00 00  00 00 00 00  00 00 00 00  00 00 00 00  C6 39 F0 00  C7 22 5F 00  C7 74 0B 00  .................9..."_..t..
Position hex meaning
00-09 55 43 53 46 20 4E 4D 52 00 00 UCSF NMR
10-13 02 01 00 02 2 dimetion, real data, 2 for current format
180(B4)-185 31 33 43 00 00 00 13C (Carbon 13)
188-191 00 00 04 00 1024 data points
196-199 00 00 00 80 tile size 128
200-203 42 FB 8B 64 125 MHz
204-207 46 A2 20 D8 Spectrum width 20752.4219 Hz
208-211 42 96 03 2B Center of spectrum 75 ppm
308(134)-313 31 48 00 00 00 00 1H (proton)
316-319 00 00 04 00 1024 data points
324-327 00 00 00 80 tile size 128
328-331 43 FA 13 85 500 MHz
332-335 45 DF 36 DB Spectrum width 7142.857 Hz
336-339 40 A0 00 40 Center of Spectrum 5 ppm

The header for carbon 13 starts at 180. The header for proton starts at 180 + 128 = 308. The data starts at 180 + 128 + 128 = 436.

The number of points among each axis is 1024, and the tile size is 128. So the number of tiles among each axis is 1024 / 128 = 8.

The tiles are saved in 1D vector, if we reorganize the 1d vector into 2D matrix, we will have the following:
1 2 3 4 5 6 7 8
9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32
33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48
49 50 51 52 53 54 55 56
57 58 59 60 61 62 63 64

The data in each tile is also saved in row order. So if we have 64 data points in each tile and want to reorganize the data into 2d matrix, the data will also looks like the table above.

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