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To-do list

by Tim Stevens last modified 2009-11-16 14:56

A list of proposed upcoming additions and changes to CcpNmr Analysis

Note this list is in no particular order and relates to CcpNmr Analysis version 2 only.

Estimate order parameters (Mark Howard)

  • Model-free formalism

Incremental project backup

  • To gzipped XML files

Hertz scales *Mostly done as of v2.1.1

  • On spectrum window axes maybe (Wayne)
Analysis Profile Extensions (Tim)
  • Standard distributed profiles: Black/white/Sparky style
  • Contour colours by experiment type system implemented

Projection Spectroscopy

  • Check functions that use peak positions
  • GFT handling

Sequence finder (Tim)

  • System to search for a residue sequence substring (inc wildcards)
  • Present assignment options
  • Possible modification of Atom Browser

CcpNmr SpectrumView (Tim)

  • A simple and quick application (severely cut down Analysis)
  • Just view spectra and navigate
  • Loads minimal data model, if at all

Spectrum Groups (Wayne & Tim)

  • Allow spectra to be grouped (e.g. by Experiment Type)
  • Option for spectrum window top-panels

Spectrum Referencing (Wayne)

  • Allow old referencing values to be remembered
Hiding peak annotaions
  • Select viewing modes to control behaviour (Tim)
  • Only show annotations within a set region (Wayne & Tim)
  • Varies with window (and strip) (Wayne)

Carbohydrate functions (Tim)

  • Possible ring spin system resonance assigner (useful for protein COSY/TOCSY too)

Extend spectrum windows (Wayne)

  • Ability to 'roll' or permute axes (problem with mapped 2Ds here)
  • Tie together window scrolling?

More reference chemical shifts (Tim)

  • 2D, correlated chemical shift displays

Spectrum window display boxes (Wayne & Tim) COMING SOON

  • Lines appear at chemical shift values at the X/Y axes
  • Lines to connect peaks in the same spin system
  • User-defined regions

COSY handling

  • Dedicated saddle-point peak picker (Wayne)
  • Measure and store couplings (Tim)
  • Spectrum display of multiplets (Wayne)

NOE back calculation (Tim)

  • Estimate NOE intensities given structure
  • Include spin diffusion and relaxation analysis, given structure

Experiment types in Atom Browser (Tim, Rasmus)

  • Only display atoms which would be visible given a type of experiment
  • Type may be automatically set given a peak

Peak box widths (Wayne)

  • Integrate within box definition
  • User defined by selecting a mouse region
  • Asymmetric boxes: Possible as a window element

Last toggled peak list on top (Wayne & Tim)

  • Global option to draw the last toggled peak list last so that it appears on top
  • If not set to "ON" the drawing order follows the order attribute

Z scrollbar colours and ranges (Wayne & Tim)

  • Display Z dimension ranges for spectra in spectrum windows using coloured blocks
  • Colour comes from contour colour

Structure viewer improvements (Tim)

  • Sort out the occasional blanking. Something funny happening with Tk
  • Enable navigation from structure to resonances (and thence constraints and peaks)
  • Add cartoon ribbons, MolScript style
  • Integrate YASARA

Molecule Residue editing (Tim)

  • Allow the user to edit a molecule sequence even if assigned

RDCs (Tim)

  • Interface to measure multiplet splittings, possibly from different spectra
  • Interface to calculate residuals and link to alignment medium

Isotope labelling schemes (Tim, Frank Eisenmenger)

  • Molecule instance labelling, for mixtures, non-standard incorporation etc.
  • Population of Sample from schemes and sequence
  • Population of user-editable atom-level schemes


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