Main Panel¶
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View and Edit External NMR Calculations
This popup window is used to view the various calculations, performed by programs external to CCPN (like CING or ARIA), that have nonetheless been setup inside CCPN software to use CCPN data.
This popup is somewhat of a prototype, so its functionality is neither complete nor throughly tested, but it is the only way to get an overview of certain types of data.
The popup window is divided into two tabs. The first “Calculation Groups” tabs shows the various types of software that calculations have been setup for. It should be noted that this system is general and where possible the user should consider using the dedicated graphical interfaces to run particular pieces of software (like those in the main Structure menu).
The “Calculation Runs” tab shows the various jobs that have been setup, and possibly run, for the different kinds of software. The user can change the software calculation group via the top most pulldown menu, then change the “Run Number” to look though the jobs (“runs”) that have been setup. New, blank or duplicated, “run” specifications can be made at any time. A specification may also be deleted, but a run may only be edited if it has not been used by the calculation; a run is a record or what was done. A completed run may effectively be edited by making a copy first.
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 (if the job is editable) use the [Add ...] and [Remove ...] buttons to dictate which CCPN entities will be selected for the calculation. Not all types of data will be appropriate for all calculations; further incentive to use the specialised program interfaces when they are available, rather than this general one.
The “Run Settings” tab is filled with a table of all of the parameters that have been associated with the currently selected run. A parameter will have an identifying code and perhaps a group to collect certain parameters together. Some parameters may just represent a simple value, but others may associate a value with a “Data Object”; a CCPN data model entity containing NMR information or a reference to external data held on disk.
The “Output Data” table lists all of the CCPN entities that were generated or modified by the selected calculation job (if it were run).
It is notable that a “run” specification will persist even if some or all of the CCPN data entities (e.g. restraint lists) it was originally linked to have been deleted. In this way the user still has a record that something was run, and there is no restriction on the normal manipulation of CCPN data. If a CCPN data item has disappeared then the run will list it as “DATA MISSING”.
Documentation missing
Table 1 | |
# | Row number |
Name | name of calculation group (often a program name) |
Num. Runs | The number of calculation run specifications stored for the group (Editable) |
Add New Calculation Group: Add a new grouping (e.g. by program name) to contain calculation specifications
Delete Calculation Group: Delete the selected calculation group (program settings) and all calculation run settings it contains
Documentation missing
Calculation Group: Selects which program (or other calculation grouping) a set of calculations relate to
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
Documentation missing
Molecular System: Selects which molecular system the calculation will be run on
Run Details: User-editable textual comment for the current calculation
Documentation missing
Table 2 | |
# | Row number |
Mol System | Code for the molecular system to which the structure relates |
Ensemble | The id number of the structure ensemble within its molecular system |
Models | The numbers of the conformational models considered |
Remove Selected Models: Remove the selected structural models from consideration (does not delete the coordinates)
Add Ensemble: Add the selected structure ensemble as calculation input
*None*: Selects a structure ensemble which may be added as calculation input
Add Model: Add the selected conformational model to the calculation input
*None*: Selects a conformational model which may be added as calculation input
Documentation missing
Table 3 | |
# | 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
Documentation missing
Table 4 | |
# | 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
Documentation missing
Table 5 | |
# | 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
Documentation missing
Table 6 | |
# | The serial number of the parameter; an internal CCPN numbering |
Code | The identifying code (one word name) of the parameter |
Group | The group to which the parameter belongs |
Name | Human reasable name or decription of the parameter |
Value(s) | The current value associated with the parameter |
Data Object | Documentation missing |
Documentation missing
Table 7 | |
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 |