These use cases describe how to run MDDnmr jobs on the eNMR grid.
Gzipped tar files containing all the necessary files and an example of a job file for grid submission are provided for download. These use cases provide a basis for executing any MDDnmr job on the eNMR grid.
File: mddnmr_hncoca.tgz
Description of content:
This directory contains an example of using MDDnmr v1.6 software for processing of a non-uniformly sampled spectrum 3D HNcoCA using Multi-Dimensional Decomposition (MDD).
Created by Victor Jaravine / Henry Jonker, BMRZ, May 2009
Input files:
- mddnmr.jdl : job file for grid submission
- mddnmr.run : executable script that will run the program
- 284hncoca.tgz: gzipped tar file containing the input spectrum (need unpacking also before this run) and processing parameter files to be executed
Output files:
- mddnmr_output.tgz : output of MDDnmr processing
Execution on the eNMR grid: (commands are in italics)
1) Login as an eNMR grid user:
voms-proxy-init -voms enmr.eu
2) Download all example data into some location.
3) Submit job file:
glite-wms-job-submit -o mddnmr.jobid -a mddnmr.jdl
4) Check status:
glite-wms-job-status -i mddnmr.jobid
5) When finished get back output:
glite-wms-job-output -i mddnmr.jobid --dir mddnmr-output
Comments :
The program "MDDNMR 1.6" is free for academic use: both on the "eNMR" GRID and downloaded to PC. Recently revised documentation describes a number of new and old features plus several examples of processing of 2,3,4Ds. Further information can be found on the Google groups site of MDDnmr. Please, feel free to post your comments and suggestions to the group by sending email to mddnmr@googlegroups.com (You can post from any registered email address, not just gmail). Best Regards, Vladislav Orekhov, Victor Jaravine
Other examples :
Other examples can be executed on the eNMR GRID in exactly the same way as the above example (3D HNcoCA), using the same GRID submition/retrieval scripts, but different name for the data fid and other parameters set in the envocation shell script. Several more examples, described in the documentation can be downloaded directly from site of SNC-Hasselblad-lab. (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
Publications (downloads):
The method of recursive-MDD used in the software versions 1.5+ is presented here:
Jaravine V, Ibraghimov I & Orekhov V, Removal of a time barrier for high-resolution multidimensional NMR spectroscopy Nature Methods, 2006, 3:605 - 607.
The demonstration of HD-MDD on two biomol systems given here:
Jaravine V, Zhuravleva A, Permi P, Ibraghimov I, Orekhov VY. Hyperdimensional NMR spectroscopy with nonlinear sampling. J. Am. Chem. Soc. 2008, 130:3927-36.