Hello,

Finally we have a 2.1 release of Analysis and the FormatConverter.  This
took longer than it should have because the Analysis part of the data
model has changed between 2.0 and 2.1, to allow some new functionality to
be added in the near future.  So it will allow multiple windows per
spectrum window, so to speak.  In the jargon of the data model, the whole
window is a SpectrumWindow and the sub-windows are SpectrumWindowFrames.
By default there is only one SpectrumWindowFrame per SpectrumWindow.

We hope we've removed most of the bugs associated with this transition
(well, for the one SpectrumWindowFrame case), but quite possibly there are
still some remaining.  And there have been many other changes, all of
which could introduce bugs (I was chasing one around this morning).

So far I've put source code releases and pre-compiled releases for 64-bit
Linux and OSX Intel on the download page at:

   http://www.ccpn.ac.uk/ccpn/software/downloads-v2

I'll do more releases shortly.

You will have to download the release from this webpage to get it, so you
will not be able to download it from inside Analysis via the Project -->
Updates menu item.

The releases will unpack into ccpnmr/ccpnmr2.1 so you can keep existing
1.0/2.0 releases in the same place, if desired.

Tim has provided a long list of changes below.  Rasmus made some changes
to the Open Spectra dialog which he is best placed to explain, but it
should allow easier opening of multiple spectra for Bruker files.  Wim can
tell you about the FormatConverter changes.

Wayne

> * There is now a Pos/Neg button in the Contours option which cycles
> between having Positive only and then Negative only and then Positive
> and Negative contours (or something like that).
>
> * Big re-write of the link seq spin systems functionality (Now renamed the
>  "Protein Sequence Assignment" section). The issue with overlapping spin
>  systems has been removed (although still requires the assignment to root
>  resonances to be correct). There are now two linking scores, one based on
>  accuracy alone, and the other scaling with the number of matched peaks.
>  Tolerances for matching/weighting can now be specified for each spectrum
>  independently (this is the same as the general assignment tolerance).
>  Also, you can now match 1H and 13C strips at the same time, i.e. with with
>  a HNCO/CA/CB system and a HN(co)HA/HB system of spectra together.
>
> * Big overhaul of the amino acid type prediction routines. The system is now
>  _much_ less forgiving of bogus shifts in a spin system, but is much more
>  precise. The system now takes account of experiment types (e.g. something
>  in HNcoCACB can only be CA/CB) and "onebond" relationships, i.e H-C pairs
>  are typed together for more indicative scores.
>
> * Added ability to assign, set type & set tentative assignments for a pin
>  system when selecting residues in the atom browser (rather than just
>  assigning atoms for resonances)
>
> * Closed popups will no longer be updated until reopened. This leads to
>  general speed increases across the GUI.
>
> * Add ability to change peak position units between ppm, point & Hz in peak
>  tables
>
> * Added option to assign all NOE peaks in the whole peak list according to
>  the shift/distance filtered assignments displayed in the NOE Contributions
>  assignment system (formerly "Link NOES")
>
> * Added ability to display peak connections and a table of peaks from atoms
>  selected in the structure viewer. Very useful for resolving prochirals.
>
> * Added ability to delete a single assignment contribution in the NOE
>  Contributions (formerly "Link NOES") assignment table.
>
> * Added a new, hopefully more intuitive, way of swapping reference expt
>  dimensions, e.g. when Analysis guesses wrongly which dimension is bound to
>  which. The new table shows pairs of dims and says what the relation ship
>  between them is, and allows you to swap where appropriate.
>
> * Added option to import data from PDB and BMRB (NMR-STAR) files directly
>  from the Project menu. This is not just for shifts and coordinates, any
>  sample information etc. relating to the database deposition will be loaded
>  too.
>
> * Added menu option for the ECI (via Structure menu). The Entry Completion
>  Interface allows you to collect information for a joint PDB/BMRB
>  structure/NMR database deposition. The resulting  "Entry" object can be
>  used to automatically fill most of the fields in the AutoDep web form,
>  i.e. you just upload your CCPN project.
>
> * Added fractional intensity contribution and total "NOE sum" distance to
>  the NOE Contributions (formerly "Link NOES") assignment table.
>
> * Add backbone non-H category to assignment completeness report
>
> * Add colouring experiment series by colour scheme
>
> * Added ability to quickly copy NOE tolerances and NOE bins from one source
>  spectrum to another
>
> * Added ability to have no fit function when following chemical shift and
>  peak intensity series - useful when you need to see the peak groups that
>  fail to fit
>
> * Added en masse setting of peak details. - Very useful to mark violated NOE
>  peaks.
>
> * Added ability to shift a whole peak list by a given amount in each dim -
>  useful for TROSY etc.
>
> * Added ability to update peak assignments from dist restraint lists, e.g.
>  after ARIA has generated unambiguous restraints,
>
> * Added ability to use currently selected peak for in the NOE contribution
>  assignment system
>
> * Added assignment groups to assignment panel (peakContribs). This allows
>  you to group mutually exclusive peak assignments e.g. you can say which
>  resonance goes with which other in an ambiguous situation, and thus avoid
>  linking wrong NOE pairs etc.
>
> * Added chart for amino acid CA and CB chemical shift
>
> * Added RefDB (Wishart) as a source of reference chemical shift information.
>  You can now switch between BMRB & RefDb in the graphs and charts. RefDB
>  information is now used in the residue type prediction.
>
> * Added option to clear spin system residue type in type residue prediction
>  popup
>
> * Improved spin system typing in the automated assignment routine so it now
>  makes use of i-1 spin system information (e.g. HNcoCACB).
>
> * Added system for the setting of tentative residue assignments via
>  Assignment Panel. This status supersedes any type-only specification, but
>  is in turn superseded by a full atomic/residue assignment.
>
> * Added a filter to the assignment quality reports to show only the alerts,
>  i.e. the peaks & resonances you need to focus your attention on.
>
> * Added first draft of the popup to create and administer H-bond restraints.
>  More functionality will appear in future.
>
> * Added Models tab and RMSD graph to Structures popup. - You can now see how
>  the models differ in RMSD and how RMSD varies along the sequence.
>
> * Added NMR Calculation Setup option (via "Other" menu), this will be used
>  increasingly in the future and is a generalisation of the system used for
>  CING setup and ARIA setup (not yet released).
>
> * Added ability to propagate contour levels from one spectrum to others (in
>  EditSpectrum)
>
> * Added a Python wrapper for SHIFTX, with direct CCPN object I/O. This is
>  not available via the GUI (yet) but can be accessed from
>  .../python/ccpnmr/anysis/wrappers/Shiftx.py for the more pythonic of you.
>
> * Added ability to specify residue ranges in the atom assignment status of
>  the quality reports
>
> * Added potential to use a sequence alignment when calculating shift
>  differences
>
> * Added structural display of chemical shift differences
>
> * Added ability to calculate shift differences by direct shift list
>  comparison, rather than having to have the shifts on peaks.
>
> * We now allow use or HNCO & HNcoCA root spectra when picking & assigning
>  other spectra from root resonance locations. - In such instances only the
>  amides are used as the root.
>
> * Enable initialisation of root resonances for 13C-HSQC spectra.
>
> * Improved copying of peak lists so that it works with a dimension mapping,
>  i.e. dim orders do  not have to be the same for matching, but there must
>  me a mappable equivalent in whatever
>
> * Allow violation calculations for HBond restraints
>
> * Lots of (hopefully invisible) changes because of changes to Analysis
>  section of data model
>
> * Copying peak assignments may now give merged assignments if two sources
>  match a single target
>
> * Disabled Residue Information option for Windows OS until we figure out why
>  it is broken for this OS. order.
>
> * Restriction of restraint generation to non-synthetic peak lists
>
> * Various popup & menu name changes. - Hopefully more informative.
>
> * Simplified the copy molecule assignments functionality to use "operations"
>  rather than "source" and "destination" chains.