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
Run Number: Selects which calculation job or “run” is currently being viewed or edited
New Run: Make a setup for a new calculation run
Copy Run: Make a new calculation run by copying the current one
Delete Run: Delete the current calculation run settings
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
Structures
Documentation missing
Ensemble: The structure ensemble coordinates to submit
Table 1 |
Model |
Conformational model number |
Use |
Whether analyse this model (Editable) |
Activate Selected: Activate the selected models so that they will be consedered in the analysis
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 |
Remove Selected: Remove the selected measurement list from consideration (does not delete the data)
Add Measurement List: Add the selected measurement list as calculation input
*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 |
Remove Selected: Remove the selected peak list from consideration (does not delete the data)
Add Peak List: Add the selected peak list as calculation input
*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 |
Remove Selected: Remove the selected restraint list from consideration (does not delete the data)
Add Restraint List: Add the selected restraint list as calculation input
*None*: Selects a restraint list which may be added as calculation input
Run Settings
Documentation missing
Server Job Submission
iCing URL: Web location of iCING server to use
Results File: Name of file to store compressed CING results in
Choose File: Select file to overwrite with CING results
Results URL: Web location where CING results will be posted
View Results HTML: Open the HTML CING results in a web browser
Submit Project!: Submit the CCPN project to the CING server
Check Run Status: Determin whether the iCING job is complete, pending or has failed
Purge Server Result: Remove all trace of the last submissionfrom the iCING server
Download Results: Download the compressed CING results, including HTML
Residue Options
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) |
Activate Selected: Use the selected residues in the analysis
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 |