To-do list
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)
- 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
- 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