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Data Management in CCPN

A document detailing where different types of information can be found in a CCPN project.

Project Summary Table

Analysis contains a summary table listing the project directories, spectra, peak lists, molecules and chains, restraint lists and structure ensembles contained within that project. This can be accessed using M:Project:Summary. The data contained in this table can also be displayed in a web browser for easier viewing of the entire table and printing. Moreover, specific sections of the table can be exported into text files by clicking the right mouse button on the desired section and selecting export. This will then bring up a dialogue box, in which the name, format and location of the export files can be specified. Unless a specific location is specified by clicking the File: button, the data will be exported to the directory from which analysis was launched.

Experimental Details

CCPN divides experimental information in two: the Experiment (data as acquired), and the DataSource or spectrum (data as processed). You could (but rarely do) have several processed DataSources for a single experiment.

Information concerning a specific experiment can be found under M:Experiment:Experiments. This dialogue box contains five tabs, under which different information is available. The Experiments tab contains the number of dimensions, CcpNmr Experiment type, the shift list associated with each experiment, the Molecular System(s) associated, information concerning the data source, Shift referencing and the number of spectra associated with that experiment. There is also a details field in which a user can insert any relevant comments, such as date of acquisition, lab book reference. All fields containing an E in the bottom left hand corner are editable. In the Experimental Details tab, information relating to the Spectrometer, Probe and sample can be input and displayed. Sample volume, Num. Scans, NMR Tube Type, Spinning Angle and Spinning rate are free text fields, Sample State and Volume Unit are drop down lists and Spectrometer and Probe are also drop down lists, but are populated by information in the NMR Instruments tab. Chemical Shift referencing information can be included under the Shift References tab and Instrumental Details can be input under the NMR Instruments tab.

Data Locations and Referencing

The spectra dialogue box found under M:Experiment:Spectra contains information about the processed spectra , such as numbers of peaklists, noise level, data type, referencing in each dimension, file details and data locations.

Measurement Lists

Any set of measurements performed as part of spectral analysis, such as T1 relaxation lists, Heteronuclear NOE lists and chemical shift difference lists are found under M:Data Analysis:Measurement Lists. Shift lists are in principle Measurement Lists too, but can be found more prominently under M:Resonances. Note that different shift lists are used for different groups of experiments (e.g. acquired at different temperatures).

Structures

Structures imported into a CCPN project can be found under M:Structures:Structures. This dialogue box contains five tabs with different information about structural ensembles imported into the project. The first tab, {Ensembles} shows a list of all ensembles with number of structures, RMSDs, violation lists, number of models, chains and number of residues. In the {Structure Models} tab, if an ensemble has been merged and superposed, a graph showing the RMSD to mean of backbone and all atoms across the ensemble.  The {Residues} tab contains the values of the backbone and all atom RMSDs per residue, along with the Ramachandran region and the Φ and Ψ angles. The {Coords} contains the coordinates of all atoms per model and the drop-down lists; Ensemble and Model are used to select specific models in different ensembles. Finally, the {Compare Ensembles} displayed a list of RMSDs between ensembles as an n x n matrix for both backbone and all atoms depending on which radio button is selected. CCPN analysis also has a structure viewer found in M:Structure:Structure Viewer. This enables a user to view the individual members of an ensemble and to colour the structure by RMSD of H, CA, CB, O, backbone and all atoms by selection from the drop-down list next to the [Display params] button and clicking that button.

Restraints and Violations

All restraints contained within a CCPN project are grouped as Restraint Sets and these can correspond to a structure calculation import, or a set of restraints created within analysis and this information can be found in M:Structure:Restraints and Violations. The restraint group serial and the numbers of restraint lists in each group are shown in the {Restraint Sets} tab. The {Restraint Lists} tab displays the type, name and number of restraints in each restraint list within a specified restraint set. If violations have been calculated for a particular restraint list, restraint list will be coloured according to the number of ensemble members in which that restraint is violated. Restraints coloured light green indicates that this violation occurs in less than 10 % of the ensemble, yellow indicates that this violation occurs in 10-30 % of the ensemble, orange indicates 30-60 % and red indicated that this violation occurs in more than 60 % of the ensemble. The {Violation Lists} tab shows all violation lists that have been calculated in that project with the numbers of violations and the structure ensemble for which the violations were calculated. The final tab, {Violations}, lists information on violations in a particular violation list selected in the drop down list, Violation List.

Structure Calculation Data

All data relating to a CYANA structure calculation that was executed from Analysis can be found in M:Other:Nmr Calculations. Calculation Runs contains a complete set of all the calculations executed within that project. The Input Data tab contains four sub-tabs under which information pertaining to shift lists, peak lists and restraint lists used in the structure calculation and the Run Settings contains information relating to how the calculation was set up initially, including the file names of all input data, the file formats and the program specific settings. The output data table shows the file names and related CCPN object names of all data output from the structure calculation and the Summary Table contains the contents of the final.ovw file and the cyanatable of the structure calculation. Calculations done with other programs will appear in the same place, but information gathering is not so far advanced for any program other than CYANA.

Data Quality

A quality report for all assignment data in a project can be found under M:Assignment:Quality Reports. This dialogue contains four tabs pertaining to different levels of assignment. In the Atom Assign Status tab, the degree of assignment by atom type and residue type is displayed along with minimum, maximum and mean shift values for each atom. The Through-Space Status shows which residue numbers are connected to each residue in the sequence along with the numbers of short-range, long-range, intra/inter chain and sequence through space assignments. The Resonances and Peaks tabs enable identification of potentially problematic resonance and peak assignments. In the case of resonances, the BMRB mean and Random Coil values for each atom type are displayed and the SD and Maximum peak deviation between the averaged chemical shift and the peak dimension assigned to that resonance. The show only alerts tick boxes in both the Resonances and Peaks enable identification of any resonances/peaks that may be problematic in some way. This might be because a shift is assigned to peaks that are too far apart in frequency, because an assignment does not match the standard BMRB values, or because assignments are incompatible or chemically impossible.