A worldwide e-Infrastructure for NMR and structural biology

Getting started with iCing

iCing is the web server to run the CING software on your own structure and experimental NMR data. Please take a look at an example CING report from the NRG-CING site that contains all 9,000+ PDB entries. For example the CING report of PDB entry 2kq3 is located here.

For your own data you can use the steps with iCing below:

1.     Prepare your data into a convenient package. Possible formats include CCPN, CING, CYANA, and PDB but we prefer CCPN data format. 

2.     Navigate to iCing which will show you the Upload page.

3.     Click the Choose File button and navigate to your CCPN .tgz file. The file will automatically be uploaded to the server and a message will show you so when the upload has finished. A small example input file (shown at the end of the line with file name 1brv.tgz) is given for you to try out the service so you can try out the service without your own data first.

4.     Click on the Forward button at the bottom of the page to get you to the Criteria page.

5.     You can change any criteria here to your liking although we suggest you maintain the defaults shown. 

6.     Click on the Forward button at the bottom of the page to get you to the Options page.

7.     You can change the terseness of the logging and select only those residues or models to your liking although we suggest you maintain the defaults shown. 

8.     Click on the Forward button at the bottom of the page to get you to the Run page. If you maintained the defaults in the previous Criteria and Options pages you might want to consider going directly to this Run page next time. You can do so by selecting Run from the tab menu at the top of the screen.

9.     Click on the Submit button to start the creation of the report. This will bring you to the Log page where you can get a live view of the program as it is running. Simply hit the Update button when you want to get additional log information. Any WARNING and ERROR messages will direct your attention if present. They are almost never fatal so your report will be created. At his point you should expect to wait for about 30 minutes for an average project. The example 1brv project takes only 3 minutes to validate.

10.   When you hit the Update button and CING has finished you'll be directed to the Report page.

11.   Now you can click on the results here link or download the self-contained report in a zip file.

 

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life