posted by Victor Jaravine
The MDDNMR web-portal performs reconstruction and processing of Non-Uniformly Sampled (NUS) NMR experiment data uploaded via a standard web-browser.
Usage of the eNMR server: http://www.e-nmr.eu/webportal/ requires registration (free for all academic users). In addition, using the GRID high-performance computation infrastructure requires a valid personal certificate. For information on how to obtain such a certificate please refer to: http://www.enmr.eu/eNMR-registration
Required software for local viewing of results
nmrDraw (is part of nmrPipe package http://spin.niddk.nih.gov/NMRPipe/ ), or any other spectra visualization software that can read nmrPipe format data, for example, CCPN http://www.ccpn.ac.uk/ccpn/software/ccpnmr-suite, CARA http://cara.nmr-software.org/downloads/, iNMR from “Mestrelab Research”, Sparky, etc.
Relevant web sites
http://groups.google.com/group/mddnmr/
http://www.e-nmr.eu/mdd-portal/doc/Welcome.html
The MDDNMR web server tutorial
Brief description: In this tutorial you will perform reconstruction and processing of one example of processing of 5% NUS 3D HNCO.
First, using the web interface input data file is uploaded (tar or tgz of directory of the NUS spectrum, as is with FID and all other parameter files). Besides, two nmrPipe scripts are uploaded - for processing from time-domain to frequency-domain. And after calculation is performed, the result of processing can be downloaded and viewed.
Prepared are 5 examples of NMR experimental data of varying spectral dimensionality, but in this tutorial we provide step-by-step description only for the 1st example: 3D HNcoCA (the details of the datasets are given in next sections).
3D HNcoCA
2D HMQC
4D NOESY
3D 15N NOESY-HSQC
3D HNCA
Required input data:
In order to run this tutorial, download the data by following link webmdd_hncoca_fid.tar
Unpack this file in a directory of your choice:
tar xvf webmdd_hncoca_fid.tar
This will create three input files for running of the example via web-portal:
a tar-gzipped file with original FID data (recorded by a NMR spectrometer in NUS mode) 284hncoca.fid.tgz , and two conventional processing scripts for nmrPipe (by some estimates 70% of all spectra are processed with this software) fidSP.com and recFT.com
The runs:
All of these examples can be also run in UNIX line command mode, or invoked via standard gLite User Interface (UI) on the eNMR GRID. For this method of processing a couple of other files are needed, the files are listed and the procedure is described on the eNMR wiki. Here we focus only on the mode of submission via a standard web browser (Firefox recommended).
More detailed documentation for “MDDNMR” can be found here http://enmr.chemie.uni-frankfurt.de/mdd-portal/Manual_1.6.htm
Note that the “eNMR” wiki use-case for “MDD” http://www.e-nmr.eu/use-case-mddnmr describes how to run it in line mode via gLite UI.
We suggest two runs for comparison of the reconstruction quality:
Run1: check option for “sparse-DFT” processing – in this case the missing time-domain data points are set to 0, followed by regular 3D DFT (i.e. without MDD).
Run2: check option for “MDD” processing – in this case the missing time-domain data points are reconstructed by R-MDD procedure, followed by regular 3D DFT.
Submitting the data via the web-form
From http://www.enmr.eu/webportal/ go to the “MDD” web-page http://www.enmr.eu/webportal/mdd.html
Conventionally, MDDNMR performs calculation with most parameters set at default values (~40), and there is no need to learn them and change the defaults without a specific purpose. However, a dozen of parameters are shown and can be set via the portal interface, but in this tutorial we shall only change a few.
Experimental data
The first file to upload is the .tgz (tar-gzip) archive (it can be also simple .tar) containing experimental data: 284hncoca.fid.tgz (containing FID directory 284hncoca.fid with a binary data FID file, in this case Bruker ser (or fid for Varian), and all associated experimental parameters in the .fid directory (note, that we renamed and added extension .fid to Bruker name (just digits), which is actually Varian convention, but that is done only for clarity of presentation).
nmrPipe scripts
Uploading nmrPipe scrips (no modification needed)
fidSP.com - the script is used for processing of direct dimension of the fid, (as this dimension is fully sampled), prior to running mdd reconstruction of the indirect dimensions. This file is automatically generated by the spectrometer software.
#!/bin/csh
# : x1 xn data B xphase
#echo "$0 $1 $2 $3 $4 $5 "
set xa = $1; set xb = $2; set data=../{$3}.data;
set name=$4; set xphase=$5; set fid=../{$3}.fid/fid
bruk2pipe -in $fid -bad 0.0 -aswap -DMX -decim 2773.33333333333 -dspfvs 20 -grpdly 67.9858856201172 \
-xN 1024 -yN 2 -zN 720 \
-xT 512 -yT 1 -zT 360 \
-xMODE DQD -yMODE Complex -zMODE Complex \
-xSW 10000.000 -ySW 2500.000 -zSW 2500.00 \
-xOBS 600.1328168 -yOBS 150.910829 -zOBS 60.817688 \
-xCAR 4.725 -yCAR 55.843 -zCAR 115.860 \
-xP0 -213.5800 -yP0 0.00 -zP0 0.00 \
-xP1 26.200 -yP1 0.00 -zP1 0.00 \
-xLAB 1H -yLAB C13 -zLAB N15 \
-ndim 3 -aq2D States \
-verb \
# | nmrPipe -fn POLY -time -auto \
| nmrPipe -fn SP -off 0.330 -end 0.970 -pow 1 -c 0.500 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT -auto \
| nmrPipe -fn PS -hdr \
| nmrPipe -fn PS -p0 ${xphase} -p1 0 -di \
| nmrPipe -fn EXT -x1 ${xa}ppm -xn ${xb}ppm -sw \
| pipe2xyz -z -out ${data}/${name}%03d.DAT -ov -nofs -verb
exit 0
and recFT.com - this file makes DFT transform of the two indirect dimensions after the reconstruction procedure (it can used without any change for any 3D spectra).
#!/bin/csh -f
echo '##############' in $0 $1
if( $#argv < 1 ) then
echo "Use: $0 <input pipe> <template for output spectrum>"
echo "nmrPipe processing of YZ dimensions after MDD reconstruction"
exit 1
endif
set ft4trec=$1
if( $#argv > 1 ) set proc_out=$2
if( ! -f $ft4trec ) then
ls $ft4trec
echo $0 failed
exit 2
endif
echo '######### Processing time domain MDD reconstruction #############################'
echo
echo Processing YZ dimensions
showhdr $ft4trec
cat $ft4trec \
# XYZ \
| nmrPipe -fn TP -auto \
# YXZ \
| nmrPipe -fn SP -off 0.45 -end 0.98 -pow 1 -c 0.5 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT \
| nmrPipe -fn PS -hdr \
| nmrPipe -fn PS -p0 0 -p1 0 -di \
| nmrPipe -fn TP -auto \
# XYZ \
| nmrPipe -fn ZTP \
# ZYX \
##| nmrPipe -fn LP -auto -ps0-0 \
| nmrPipe -fn SP -off 0.45 -end 0.98 -pow 1 -c 0.5 \
| nmrPipe -fn ZF -auto \
| nmrPipe -fn FT \
| nmrPipe -fn PS -hdr \
| nmrPipe -fn PS -p0 0 -p1 0 -di \
| pipe2xyz -out $proc_out -x -ov
# ZYX
echo $proc_out ready
exit
Important: Check the option "Bruker " for this example. Currently MDDNMR uses two naming notations for the root name of the NUS files: nus_3dsetup (Bruker) and nls (Varian).
Change other parameters
The parameter that is usually changed is “ROI size (ppm)” (ROI - Frank Delaglio term, Region-of-Interest). Change it from “0.45” to “1.0” for example, it is the size for the extract from the direct dimension. Thus with “leftmost point ...” set at “8.75”, the region of interest “1.0” corresponds to the 1H range 8.75-7.75ppm.
Job submission
As a final step, enter your username and password and press Submit. If everything went correctly, MDDNMR will provide you with a link to the result. The page will check if you entered your parameters correctly. If error has occurred during calculations, it will be in the output std.err file.
Viewing the results
Since we are calculating a 1ppm extract of a relatively small 3D spectrum, the MDDNMR runs should take a minute or two, or more depending on the server current load and length of the jobs queue. Once the run is finished, it is Ok to unpack the resulting file, and check the results.
Visual inspection and comparison
Visual inspection of the results is an important part of the analysis. You can view the quality of reconstructed and DFT processed spectra - by viewing in nmrDraw (or other program) the 3D itself: files ./ft/tdrec0??.dat in nmrPipe format, or better by viewing three 2D projections: N15.1H.dat N15.C13.dat 1H.C13.dat
If you performed two runs, unpack them into different locations (or rename), and compare the spectral quality looking at the same plane, e.g. N15.C13.dat. There are approximately 20 times more noise in the “sparseDFT” case, which is a very noticeable difference.
You could check this fact quantitatively by running a noise estimation procedure (e.g. “Estimate noise” in the “Draw” menu of nmrDraw).
Additional runs
After the initial experience you could try other examples (this is not intended but possible for the 4/5 November 2009 Cambridge CCPN/EBI/ENMR workshop). The examples can be executed on the eNMR GRID in exactly the same way as the above example (3D HNcoCA), using the web-form submission/retrieval, but different FID and the different nmrPipe scripts. Several more examples, described in the documentation, also can be downloaded from the site of SNC-Hasselblad-lab. (When downloading, please, note that some files have large size):
3D HNcoCA: 284hncoca.tgz (6.0 Mb), Ubiquitin (Bruker data)
Jaravine V, Zhuravleva A, Permi P, Ibraghimov I, Orekhov VY. J. Am. Chem. Soc. 2008, 130:3927-36
2D HMQC: HD384_plasma_gChsqc.tgz (11.7 Mb) VDAC (Bruker data)
Hiller et al. Science 321, 1206-1210 (2008)
4D NOESY: A_63_VDAC_25demo.tgz (21.0 Mb) VDAC (Bruker data)
Hiller et al. Science 321, 1206-1210 (2008)
3D 15N NOESY-HSQC: BPgnoesyNhsqc_S.tgz (93.5 Mb) 15 kDa (Varian data)
Orekhov et al. J. Biomol. NMR 2003, 27, 165
3D HNCA: az_HNCA_high_res.tgz (845 Mb) Azurin (Varian data)
Jaravine V, Ibraghimov I, Orekhov V. Nature Methods, 2006, 3: 605
Alternatively, you can run MDDNMR on your own data, if you have recorded experiments in NUS mode. In the latter case, one need to upload a corresponding tarred fid, and use fidSP.com located in the *.fid/proc/ directory (it is automatically created by the spectrometer software. it is also possible to create such file manually: via “copy-paste” from the file “fid.com” produced by running the program “bruker” in the FID directory from the “nmrPipe” package). For most 3D cases recFT.com can be used without modification. Alternatively, the scripts can be prepared manually by modification from the examples of the corresponding dimensionality.
