Other : NMR Calculations

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”.

Main Panel

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Calculation Groups

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)

button Add New Calculation Group: Add a new grouping (e.g. by program name) to contain calculation specifications

button Delete Calculation Group: Delete the selected calculation group (program settings) and all calculation run settings it contains

Calculation Runs

Documentation missing

pulldown Calculation Group: Selects which program (or other calculation grouping) a set of calculations relate to

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

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

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

button Remove Selected Models: Remove the selected structural models from consideration (does not delete the coordinates)

button Add Ensemble: Add the selected structure ensemble as calculation input

pulldown *None*: Selects a structure ensemble which may be added as calculation input

button Add Model: Add the selected conformational model to the calculation input

pulldown *None*: Selects a conformational model which may be added as calculation input

Shifts & Measurements

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

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 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

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 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

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

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

Output Data

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

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