WARNING: this is a beta version. Please report all problems to the CCPN development team.
About
The CcpNmr Grid Portal was designed to facilitate the calculation of 3D structure of biomolecules from NMR spectroscopy data.This portal is based on CCPN Data Model, ARIA and CONDOR, running on CamGrid and is available for not-for-profit users only.
If you use this resource, please cite Fogh RH, Boucher W et al. (2005). Bioinformatics 21, 1678-1684; Vranken WF et al. (2005). Proteins 59, 687-696; Rieping W et al. (2007). Bioinformatics 23, 381-382 and Nilges M et al. (2008). Structure 16, 1305-1312.
Disclaimer
This service is provided with ABSOLUTELY NO WARRANTY and holds no liabilities. If you decide to use it, bear in mind that your data and potential results are not stored with encryption, and the service administration has access to it. Furthermore, the data and results will be eventually removed after two weeks from the time of submission, whether your job has finished or not.Beta version
This is the beta version of the CcpNmr Grid webserver and is not production stable. Please feel free to try it and report any bugs or strange behaviour to the Administrator.What the CcpNmr Grid does
All you need a is a CCPN project compressed with Zip or Tgz. If you don't have a project already, you can get one by converting your data via FormatConverter portal. If your CCPN project is in the old API (1.x), convert it to the new CCPN API (2.x) at CCPN v1 to v2 Data Upgrade Form. Once you have uploaded your project, it will be parsed and analysed, in a process that may take up to few minutes depending on the complexity of your project. Once done, a new page with options based on your project will be returned. Select the proper options and then submit. You can follow your project at Status page.What the CcpNmr Grid doesn't do
This portal is basically an web interface for ARIA, but limited. Which means that you are basically running a calculation with 8 iterations and 20 structures, plus 10 structures water refined, where only protein and nucleic acid are allowed. Molecular systems with unusual chemical compounds will fail. For restraints, only distance, dihedral and hidrogen bonds are selectable.However, if you are familiar to ARIA, you can create a customised ARIA xml file for you project, compress it with your CCPN project and once you have uploaded your file a option to select your customised ARIA xml file will be available. Select it and submit. If you do this, selecting any other parameters will be completely ignored.
With a customised ARIA xml file you can do almost everything what ARIA does with few exceptions like using a initial PDB file or any feature that demands extra files in your ARIA project.How CcpNmr Grid web interface works
The web interface was designed to be simplest way to obtain 3D structures from a CCPN project, by intuitive steps. The steps are:
- Compress your CCPN project
- Upload it, optionally add a title
- Select options and submit
- Follow the job status
- Retrieve results when job finished
Documentation and help
It is on the way. For the moment you can look at old version of documentation but which still keeps the same concept.More help? Don't hesitate: Administrator