Run CING from Analysis

Analysis allows you to directly upload data from the project to the structure validation software suite CING through the iCING server. CING can perform many different kinds of NMR and structure based analyses, including: PROCHECK, ShiftX, DSSP, WHAT_CHECK, Wattos etc. The CING functionality is accessible via M: Structure: CING: Validate Structures. This opens the CING Setup popup, from which projects are sent to the iCING server. To send a project to the iCING server from the CING Setup popup, do as follows: 

• • Click the green [New Run] button in the upper right corner to define the run number. This run specification will contain all of the data that CING will analyse.

  • Set Ensemble in the upper left corner to fill the {Structures} tab with various models from an ensemble.

  • Move on to the {Shifts & Measurements} tab. Choose measurement lists from the lower right pulldown menu and click [Add Measurement List] to add them to the CING analysis.

  • Move to the {Peak Lists} tab and add the peak lists to the CING analysis by selecting them from the lower right pulldown menu and clicking [Add Peak List].

  • Go to the {Restraint Lists} tab and add restraint lists to the CING analysis by selecting them from the lower right pulldown menu and clicking [Add Peak List].

  • All input data should now be set so move on to the {Run Settings} tab in the upper menu:

• • Choose “https://nmr.cmbi.ru.nl” as the “iCing URL:” in the ‘Server Job Submission’ section and set any other parameters of interest. In the ‘Residue options’ section it is possible to select residues that are to be used in the CING analysis.

  • Press the blue [Submit Project!] button to submit your data to the iCing server. The validation may take some time but a popup will appear on the screen when the job is done.

Click [Check Run Status] to view the status of your submitted project. When the job is done at the CING server it is possible to download the results through [Download Results], or to view to results on the web through [View Results HTML]. To specifically force the iCING server to remove all of the user’s data from its system, [Purge Server Result] can be clicked. Otherwise the results will be available on the CING website until the server does its next data clean-up.

For more information see the CING home page.