Protocol full text hidden due to copyright restrictions
Open the protocol to access the free full text link
Overview of the hierarchical data structure of an AnalysisAssign project. The data objects cover all data that can be stored in a project. A Spectrum is an object containing the path to the stored NMR data file and all the stored properties of that data. A PeakList is a child object of a Spectrum and serves as a container for Peak objects, which contain all position, intensity and assignment information. A SpectrumGroup combines multiple Spectrum objects, so they can be treated as a single object. A Sample corresponds to an NMR sample and is made up of SampleComponents, which indicate the individual chemical entities that make up that Sample, e.g. protein, buffer, salt, and their concentrations. A Substance object represents a defined chemical entity. A Chain object corresponds to a molecular chain, made up of Residues, which in turn are made up of Atom objects. A Complex is a container for multiple chain objects. NmrAtom objects serve as a way of connecting a named nucleus to an observed chemical shift; peaks are assigned to NmrAtoms. NmrAtoms are grouped into NmrResidues, which in turn are grouped into NmrChains. A ChemicalShiftList object is a container for ChemicalShift objects, which represent observed chemical shifts. DataSet objects serve to group RestraintLists and other input and output from a calculation, with the Data object storing links to the data structures used (PeakLists, Spectra, StructureEnsembles etc.) and associated calculation parameters. A RestraintList contains Restraint objects of a specific type (distance, dihedral, etc.). Restraint objects contain the measured value of that restraint, information for force field calculations, and the Atoms involved in the restraint. CalculationStep objects are used to track the calculation history of a DataSet, with the programs used for previous steps and their input and output DataSets. A StructureEnsemble object is a container for ensembles of coordinate structures, with each coordinate structure defined by a Model object. Notes are objects that contain free-text information to be stored in a project
Different data formats that can be loaded and parsed by AnalysisAssign
Format | Drop on sidebar | Load via menu | Drop onto module | Action |
---|---|---|---|---|
CCPN version 2 project | ✓ | ✓ | ✓ | convert to version 3 and load project |
CCPN version 3 project | ✓ | ✓ | ✓ | load project |
NmrPipe | ✓ | ✓ | ✓ | loads and displays spectruma |
Azara | ✓ | ✓ | ✓ | loads and displays spectruma |
Bruker | ✓ | ✓ | ✓ | loads and displays spectruma |
Varian/Agilent | ✓ | ✓ | ✓ | loads and displays spectruma |
NmrView | ✓ | ✓ | ✓ | loads and displays spectruma |
XEASY | ✓ | ✓ | ✓ | loads and displays spectruma |
UCSF | ✓ | ✓ | ✓ | loads and displays spectruma |
FASTA | ✓ | ✓ | create molecule(s) from sequence | |
PDB-v3 | ✓ | ✓ | load structure(s) | |
NEF | ✓ | ✓ | parse contents and load into project | |
comma separated file | ✓ | ✓ | parse contents and load if possible | |
Excel spread sheet | ✓ | ✓ | parse contents and load if possible |
aWhen dropped on spectrum display module
SUD criteria positivity rate. *if there are missing data for some items, the number of patients concerned is mentioned below. DSM SUD criteria: Item 1 = Using more of a substance than planned, or using a substance for a longer interval than desired (missing data for 2 patients). Item 2 = Inability to cut down despite desire to do so (missing data for 2 patients). Item 3 = Spending substantial amount of the day obtaining, using, or recovering from substance use (missing data for 1 patient). Item 4 = Cravings or intense urges to use (missing data for 1 patient). Item 5 = Recurrent substance use may result in a failure to fulfill major role obligations at work, school, or home (missing data for 1 patient). Item 6 = Persistent usage despite persistent or recurrent social or interpersonal problems. Item 7 = Giving up or cutting back on important social, professional, or leisure activities because of use. Item 8 = Using in physically hazardous situations, or usage causing physical or mental harm. Item 9 = Persistent use despite the user's awareness that the substance is causing or at least worsening a physical or mental problem. Item 10 = Tolerance: needing to use increasing amounts of a substance to obtain its desired effects (missing data for 2 patients). Item 11 = Withdrawal: characteristic group of physical effects or symptoms that emerge as amount of substance in the body decreases (missing data for 2 patients)
(N=339 patients*)
Chemical identity
Description of manufacturing process of substance/FCM
Physical and chemical properties
Intended uses
Existing authorisation(s)
Migration of the substance
Identification and migration of impurities
Identification and migration of oligomers and reaction products