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Analysis Tasks Analysis

Subdivision of Analysis functionality into tasks with dependences between them. Rasmus Fogh 2010

This is a proposal for dividing Analysis into semi-independent areas, and shows the prerequisites for the areas. Key areas that open up further functionality are in bold. The point is to identify functionality  that can be put into Analysis Lite while more complex areas are skipped.

 

Summary

  • Proper assignment requires  all the complex functionality, so that anything that needs proper assignment must have it as well. This does limit the scope for simplification
  • The following tasks could be done without the full, complex functionality:
    • Existing
      • Using external programs in the NMR pipeline
      • Spectrum display
      • Data Analysis (Relaxation, titration etc.)
    • New
      • Spectrum overlay and comparison
      • Screening and metabolomics
      • Bespoke small-molecule assignment.

 

Task Division

 

Project

Menu: Open Project.

Contains: Import, FormatConverter, customisation

Depends on: nothing

 

NMR pipeline

Menu: M:Other:NMR Calculations; M:Structure: CING, ECI.

Extend-NMR interface

WMS

Depends on: Project

 

Macro Programming:

Menu: Macro

Depends on: Project

 

Spectrum display

Contains: Spectrum open, Window display

Menu: M:Experiment, M:Window

Depends on: Project

NB Requires streamlining of ExpPrototype and axis determination

 

Spectrum Overlay, 1D and nD

Contains: Std display plus commands for shifting spectra, differences, etc.

NEW!

Depends on: Spectrum Display

 

Screening

Contains: Match, decompose, compare to reference, metabolomics

Depends on: Spectrum Overlay

NEW!

 

Molecule

Depends on: Project

Contains:

    • Single Molecule: Select and read single ChemComp, import from Mol2 and PDB.
      No mention of MolSystem

    • Linear Polymer: Single chain protein, DNA, RNA, DNA amd RNA duplex.
      No mention of MolSystem

    • Arbitrary Molecule: Full capabilities: MolSystems, Chains, links, ...

 

Peaks

Contains: Peak Picking, Annotation, Pick Roots

Menu: M:Peaks

Depends on: Spectrum Display

 

Data Analysis

Menu: M:Data Analysis

Contains, Titrations, relaxation analysis etc.

Depends on: Spectrum Display

 

Small Molecule Assignment (1D and 2D heteronuclear spectra)

Contains: Clickable molecule diagram for assignment, Assign entire peak at once, multiplet handling.

NEW!

Depends on: Spectrum Display, Single Molecule

 

Assignment (includes Spin Systems)

Contains: Spin Systems, Resonances, Measurement Lists, Molecules, peak match, strips, tiles, etc. Homonuclear 2D assignment

Menu: M:Resonance (NB!), Molecule (NB!) M: Assignment :Assignment (NB!); M:Assignment, Copy Assignment (NB!), RightM: Mouse Window, M:Assignment Assignment Graph, M:Assignment:Quality reports

Depends on: Peaks

 

Small Molecule Identification

Contains: Making, handling and combining fragments. Building MoleculeSupport for MS, IR?

NEW!

Depends on: Assignment

 

Macromolecular Assignment

Contains: Automatic and triple-resonance assignment popups

Menu: M:Assignment, initialise roots, pick-and-assign, semiauto and auto protein assignment. M:Other:CLOUDS

Depends on: Assignment

 

Structure

Contains: including restraints, NOE assignment

Menu: Structure (except for external programs?)

Depends on: Assignment

 

The M:Charts entries should be distributed to suitable blocks.