Tutorials

Manuals for the e-NMR software and web-portals

A number of tutorials are available that describe the use of the software and e-NMR webportals:

• HADDOCK webportal tutorial:
  The tutorial describes how to model the complex of the glucose-specific enzyme IIA (E2A) and the histidine-containing phosphocarrier protein (HPr). The use of the server with various kinds of experimental NMR data (chemical shift perturbations, intermolecular NOEs and RDCs) or bioinformatic interface prediction (WHISCY, ProMate, PIER) is demonstrated. You will be guided through typical analysis steps to assess the results and will compare the effect of various data combinations on the accuracy of the generated models. A related tutorial in the form of a Flash movie can viewed here. Additional information can be found in the online HADDOCK manual.

• CYANA tutorial:
  These pages contain examples of structure calculations with CYANA.

• XPLOR-NIH tutorial:
  This page contains an example of a paramagnetic protein structure calculation with XPLOR-NIH and refinement in Amber.

• CS-ROSETTA webportal tutorial:
  This page provides a detailed explanation of the CS-ROSETTA web portal. All settings available at every step of the 3D structure generation process with CS-Rosetta are discussed together with hints on how to analyse and assess the results. Example projects ready to be downloaded as well as pre-loaded web forms are used to better explain several of the core functions.

• MD on the GRID:
  The aim of this tutorial is to introduce the user with performing molecular dynamics simulations in a GRID environment. It is not a tutorial on molecular dynamics. The emphasis in this tutorial lies on the interaction with the GRID resources and how to use these for performing protocollized molecular simulations. For this tutorial it is necessary to have access to the GRID and be logged in at an user interface (UI). GRID access can only be provided to those who posess a valid certificate and are registered the eNMR virtual organisation (VO).

• CCPN web format converter:
  An online tutorial on the use of the online format converter can found on the CCPN Biomolecular WIKI page.

• Amber REM protocol: 
  A protocol for Restrained Energies Minimization that can be performed on a pre calculated solution structure.
  

• MDD tutorial: These pages contain example of processing of a non-uniformly sampled NMR spectrum on the GRID. For other tutorials and documentation check this link.
  

e-NMR use-cases for use with the User Interface (UI)

A number of use-cases are available providing examples on how to run structure calculations on the eNMR grid with CNS, Xplor-NIH and CYANA, NMR data processing with PROSA, automated assigment with MAPPER, MARS and GARANT, scalar coupling constant determination with INFIT, and processing of non-uniformly sampled data with MDDnmr:

• CNS example
• Xplor-NIH example
• CYANA examples
  • Basic structure calculation
  • Structure calculation with manually assigned NOESY peak lists
    
  • Combined automated NOESY assignment and structure calculation
  • Homodimer structure calculation
  • Structure calculations with NOEs and RDCs
    
  • Structure calculation with NOEs and pseudocontact shifts
    
• PROSA example
• MAPPER example
• MARS example
• GARANT example
• INFIT example
• MDDnmr examples
  • NUSsampler
  • 3D HN(CO)CA, 3D NOESY ,3D HNCA, 2D 1H13C-HSQC, 4D NOESY
• GROMACS example

INFN gLite user guide

INFN Grid guides for e-NMR users and site managers