Submitting a Structure Calculation to CCPN Grid
Loading a pre-prepared project
If for any reason you are not confident about the state of your CCPN project at this stage of the demonstration before we do a structure calculation you may like to open a pre-prepared CCPN project, which has all of the expected restraints present: In the Analysis menu bar select M: Project: Open Project then [Yes] to close the current project and [No] to not save. Navigate to find and select the CcpnStructCourseC project, then click [Open].
Using ARIA in Analysis
To start the structure calculation using the restraints we have created we will launch a panel that is dedicated to setting up an ARIA job, which will be run remotely on the CcpnGrid service. The ARIA Setup popup is officially part of the Extend-NMR project, but we can avoid having to install all the Extend-NMR software and start it directly from Analysis by typing the following at the python prompt:
>>> top.activateAriaSetup()
The resulting panel allows us to control which data goes to the ARIA calculation from the CCPN project. For more fine-grained control you need to use the ARIA GUI; for example to change the annealing protocol.
Create a new job for ARIA to work on by pressing the green [New Run] button. This "Run" object links together all the data that goes into the same calculation. Ensuring that the {Input Data} and {Peak Lists} tabs are selected (they ought to be by default), change the pulldown menu at the bottom right to N-NOESY:182:1 and click [Add Peak List]; this will state that in this run ARIA should use this data. Now swap to the {Restraint Lists} tab and add restraint lists in a similar way: Select the list name from the pulldown menu and click [Add Restraint List]. Do this for all of the restraint lists, i.e. the H-bond, two distance and dihedral restraint lists:
Now that all of the input data is set we have to tell ARIA how to run on the data.
Move to the {Run Settings} tab, found at the top. Here you can see some of the settings to control the ARIA run. In the lower table make sure that the "Ambiguous protocol?" column set to "Yes" for the "Ambig" distance restraints and "No" for the "Unambig" distance restraints. If we wanted to run the ARIA structure calculation locally (noting you will have to have a CNS executable and ARIA itself available) we can [Launch ARIA GUI], make relevant changes, save the ARIA project and then [Setup Project], which will put the ARIA data in a state that it can be run from the command line in the usual way.
For this demonstration you may run the ARIA calculation remotely using the prototype CCPN Grid service. To do this simply press the [Submit to CcpnGrid] button. For this demonstration use the user identification ''test" and the password "test123". We will not wait for the final structure calculation, which will take some time (although this protein will take less than an hour on an unloaded server), but instead we will look at a structure calculation that has already been completed, and which uses exactly the same data as you have been looking at in the CCPN project.
Via a web browser go to the page http://webapps.ccpn.ac.uk/ccpngrid/status. If asked, log on with UID: ''test" password: "test123" . Here you will see various ARIA calculations, one of which will have status "Finished" and be entitled ''CcpnStructCourse...". Click on the [Results] button for this job and look at the available data. Note that we have the option to download an updated CCPN project which contains the newly calculated structures and a violation analysis, all of which remained linked to the NMR data in the CCPN project; so that for example we can easily jump from a violation to the offending point in the spectrum.