CING Setup

Setup and Submit NMR Structure Validation Analyses to CING

This popup is used to connect the data in a CCPN project to the structure validation analyses that are available at the iCING server. When submitting to this service the CCPN project (without spectrum data files) will be sent over the Internet for analysis. Many different NMR and structure based analyses will be performed under the CING platform. These include: PROCHECK, ShiftX, DSSP, WHAT_CHECK, Wattos etc.

For more information detailed information see the CING home page.

Use

To setup and run a CING job from Analysis the user first has to create a “run”, which contains all the settings. A run can be made with [New Run] or [Copy Run].

The data that relates to a job/run is divided into three sub-tabs to indicate what the input data from the CCPN project is, what settings are used during the calculation, and what the output CCPN data is. The input data is further sub-divided into various categories of data, and the user can select from pulldown menus to dictate which CCPN entities will be selected for the calculation.

Input Data

Typically to run a CING job the user will select the appropriate Molecular System from the “Input Data” panel, then select an structure ensemble in the “Structures sub-tab; these are minimum requirements for CING. The user may also a add shift lists, peak lists and restraint lists to the analysis by going into the relevant sub-tab and clicking the [Add ...] and [Remove ...] buttons to add the CCPN data entity that is selected at the bottom right of the panel.

Run Settings

The “Run Settings” tab allows the user to adjust settings that control the calculation job and actually submit all the data to the iCING server for analysis. Usually the user simply clicks [Submit Project!], assuming a run has been setup and the computer has an Internet connection. After submission the user can [Check Run Status] to get a short report, but otherwise the user will be informed when the job is complete in the CCPN interface. The CING analysis data will be available to download from the specified “Results URL” to the “Results File” by using [Download Results] Also, the data will be available for a time on the CING web site ([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.

Output Data

The “Output Data” table lists all of the CCPN entities that were generated or modified by the selected calculation job (if it were run). However, this data is not currently filled in by the CING server, although it will be at some stage in the future.

Main Panel

pulldown Run Number: Selects which calculation job or “run” is currently being viewed or edited

button New Run: Make a setup for a new calculation run

button Copy Run: Make a new calculation run by copying the current one

button Delete Run: Delete the current calculation run settings

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Input Data

Documentation missing

pulldown Molecular System: Selects which molecular system the calculation will be run on

entry Run Details: User-editable textual comment for the current calculation

Structures

Documentation missing

pulldown Ensemble: The structure ensemble coordinates to submit

Table 1
Model Conformational model number
Use Whether analyse this model (Editable)

button Activate Selected: Activate the selected models so that they will be consedered in the analysis

button Inactivate Selected: Deactivate the selected models so that they will not be considered in the analysis

Shifts & Measurements

Documentation missing

Table 2
# Row number
Data Type The kind of measurement data used and calculation input
Serial The serial number used to uniquely identify the measurement list
List Name The textual name of the measurement list
Size The number of individual measurements in the list
Details User-specified textual comment

button Remove Selected: Remove the selected measurement list from consideration (does not delete the data)

button Add Measurement List: Add the selected measurement list as calculation input

pulldown *None*: Selects a measurement list which may be added as calculation input

Peak Lists

Documentation missing

Table 3
# Row number
Experiment The name of the experiment that contains the input peak list
Spectrum The name of the spectrum that contains the input peak list
Serial The serial number of the input peak list within its spectrum
Peaks The number of peaks in the peak list

button Remove Selected: Remove the selected peak list from consideration (does not delete the data)

button Add Peak List: Add the selected peak list as calculation input

pulldown *None*: Selects a peak list which may be added as calculation input

Restraint Lists

Documentation missing

Table 4
# Row number
Restraint Type The type of restraints in the input restraint list
Restraint Set The restraint set that contains the input restraint list
Serial The serial number of the input restraintlist within its restraint set
List Name The textual name of the input restraint list
Restraints The number of restraints in the input restraint list

button Remove Selected: Remove the selected restraint list from consideration (does not delete the data)

button Add Restraint List: Add the selected restraint list as calculation input

pulldown *None*: Selects a restraint list which may be added as calculation input

Run Settings

Documentation missing

Server Job Submission

pulldown iCing URL: Web location of iCING server to use

entry Results File: Name of file to store compressed CING results in

button Choose File: Select file to overwrite with CING results

entry Results URL: Web location where CING results will be posted

button View Results HTML: Open the HTML CING results in a web browser

button Submit Project!: Submit the CCPN project to the CING server

button Check Run Status: Determin whether the iCING job is complete, pending or has failed

button Purge Server Result: Remove all trace of the last submissionfrom the iCING server

button Download Results: Download the compressed CING results, including HTML

Residue Options

pulldown Chain: Select the molecular system chain to consider

Table 5
# Sequence number
Residue Residue type code
Linking In-chain connectivity of residue
Decriptor Protonation and steriochemical state
Use? Whether to consider the residue in the analysis (Editable)

button Activate Selected: Use the selected residues in the analysis

button Inactivate Selected: Do not use the selected residues in the analysis

Output Data

Documentation missing

Table 6
Data Type The kind of data output by the calculation
# the serial number of the output data, within the calculation run
Name The name of the output data
CCPN Data The identity of any CPN objects that are lined to/as output data
Parameters Any parameters which relate to the output data
Weight Any fractional weighting that was applied to the output data