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Paramagnetic NMR

Numbat

Numbat: new user-friendly method built for automatic Δχ-tensor determination.

News - Presentation - Features – Screenshots – Poster - Download – Installation instructions – Documentation

News:

02/02/2012. Updated instructions for a Linux installation.

08/03/2009. An installer script for linux is now available. This simplify a lot the installation of required libraries (which can be sometime chalenging!). The script has been tested on Fedora 6, Fedora 10, Red Hat Entreprise Linux 4 and Ubuntu. You can request the package containing the script and all required libraries by email.

01/07/2008. Numbat v0.99 is available, you can request by email the source code for Linux (recommended) or the installer for Windows XP / 2000 (less recommended). Contact:

Presentation:

Numbat is a user friendly software that fits Δχ-tensor to a set of PCS measurements and a structure from a PDB file. It has also been designed to assist in the semi automatic process of PCS assignment. A detailed description of the software can be found in this publication: 

Christophe Schmitz, Mitchell J. Stanton-Cook, Xun-Cheng Su, Gottfried Otting, and Thomas Huber (2008). Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts. Journal of Biomolecular NMR. 41:179-189.
Article: [PDF] Supplementary material: [PDF]
Features:

Fitting of Δχ-tensors sharing the same paramagnetic center coordinates.
RACS correction term for backbone C H and N is available.
Methyl groups definition for a better prediction of PCS of 1H-methyl groups.
Pymol/Molmol display of Δχ-tensor and their isosurfaces.
Generation of PCS data set for test purposes.
Error analysis of the calculated Δχ-tensor based on a Monte-Carlo protocol.
Comparison of Δχ-tensors in various conventions.


Screenshots:

Some screenshots presenting the Graphical User Interface of Numbat:




Poster:

You can download the poster presented at the Euromar 2008 conference in St Petersburg, and ComBio 2008 in Canberra.
Download:

You can request by email the source code for Linux (recommended) or the executable for Windows XP. Write to:


Installation instructions:

Linux
Installation instructions are in the archive in the file INSTALL. As a guideline, on a Red-Hat like linux (CentOS, Scientific Linux, Fedora), prior to installing Numbat, you should get the livraries gtk2-devel, libglade2-devel and gsl-devel which you can usually do with the command (as root)

yum install gtk2-devel

yum install libglade2-devel

yum install gsl-devel

On a recent ubuntu like Linux, the librairies have slightly different name (libgtk2.0-dev, libglade2-dev and libgsl0-dev), which you can install with the commands:

sudo apt-get install libgtk2.0-dev

sudo apt-get install libglade2-dev

sudo apt-get install libgsl0-dev

It also could be that you need to install gcc compiler, if it is not already installed ('yum install gcc' or 'sudo apt-get install gcc')



Windows XP / 2000
Numbat has been designed to work on Linux systems. It has been compiled for windows; however the windows libraries used to compile it are not necessarily fully stable. You should preferentially use Numbat under Linux. If you still want to run it for windows, the installation process is very easy, just start the setup_numbat.exe file and let yourself guided through.

Mac
Installation on Macintosh should be the same than on Linux, however the installation of required libraries (and their correct version) can be more challenging. It is not recommended for the moment.



Citation:

When using Numbat, please cite the following article:

Christophe Schmitz, Mitchell J. Stanton-Cook, Xun-Cheng Su, Gottfried Otting, and Thomas Huber (2008). Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts. Journal of Biomololecular NMR. 41:179-189


Documentation:

The documentation is directly integrated into Numbat help. When you click on the help button, you get only the help relevant to the 'view' you have of Numbat.