Hello,

We've just put a new Analysis release, 1.0.3, onto the web:

  http://www.ccpn.ac.uk/downloads/downloads.html

It has lots of new features, listed at the bottom (at least those we could
remember) and some old bugs squashed, and no doubt some new bugs to find.
One thing that did not make it into this release was improved NNRPipe
support.

Wayne

Peak Find additions:

    * Added two new volume fitting methods, in addition to the existing
(poor) "parabolic fit". This can be chosen in Crosspeaks -> Peak Find
Parameters, under Other parameters. The parabolic fit is still the
default, for reasons of backwards compatibility. The two new methods are
"box sum", which just takes a sum of the values inside a box centered on
the peak, and "truncated box sum" which does the same except that it
leaves out the points inside the box which it deems like outside the box
(using the idea that if the values start to go up again then that is where
the peak ends). The box width is as specified in the Crosspeaks -> Peak
Find Parameters dialogue unless the peak itself has a box width specified
(but there is no real way of doing the latter yet).
    * Added a non-interactive peak finder, in Crosspeaks -> Region Peak
Find. This lets you specify the region (in ppm) to search in, and also
lets you exclude specified regions (e.g. the water line) inside that.
    * Added diagonal exclusion to peak finding. In Crosspeaks -> Peak Find
Parameters there is a new table at the bottom which lets you specify a
diagonal exclusion region (in ppm) by isotope type (note, not by spectrum
dimension).

Spin System typing:

    * Added a new popup to predict the type spin systems for a given
molecular system chain. This code is still in its infancy but is
functional. The spin system typing finds the global best match of spin
sytem to residue type for a given chain. The procedure uses chemical shift
information only and works with 1H and/or 13C. Sequence connectivity
information will be included in the future. The Monte-Carlo search used
can take a while to complete, but its progress does accelerate. This
system works fairly well for 1H shifts if the spin system is fairly
complete. Note that spurious resonances in a spin system makes things go
wrong, e.g. having a water shift in an ALA spin system can make it look
like a THR, so make sure your spin systems are 'clean'.
    * There is also a module to show residue type likelihoods for
individual spin systems. This is accessible from the right mouse menu, the
spin system editor and the spin system typing popup.

Spectrum Window modifications:

    * Added right mouse menu option to go to transpose positions in
windows with repeated axis types.
    * Added two new zoom options, to zoom in on the selected peaks and to
zoom to include all of the peaks corresponding to the (1st) spin system of
the current peak.
    * Added menu option to predict spin system types.
    * The order of the spectrum buttons in the top toolbar can now be set
by a spectrum order parameter (Edit Spectrum popup).
    * The orthogonal world regions (z depths) are now set according to the
width of the mapped spectra.
    * Fixed adding strip with right-mouse menu problem, where x regions
were getting confused. Centering Z planes on peak now operates on the
current column/strip.

Calculate Hetero NOE and Rates:

    * In the first instance peak grouping now takes peaks that carry the
same assignment. The reference peaks are now protected from having their
assignments changed by grouping.
    * Het NOE: Added button to show paired peaks. Added options to set
whether new peaks are picked and if matched peak pairs are to be assigned.
    * Rates: Added notification for deleted peaks in the peak rate groups.
Added "next group" funtion for convenienvce. Allow the deletion and
display of peaks that are graphed (e.g. ones with bogus intensities).

Other changes:

    * In Crosspeaks -> Copy Peak Assignments: First version of a popup to
transfer assignments between peaks in related lists.
    * There is a new system for atomSetMappings. These are now much
quicker to create and will be automatically recreated for old projects.
    * Bug fixes and improvements for spin system connectivity.
Connectivity is now NOT automatically set for spin systems assigned
independently to neighbouring residues. It is intended that sequential
connectivity is set based on evidence from HNCA/HNCOCA etc. To this end
sequential connectivity can now also be set via the right mouse menu in
the spectrum windows. Assigning one of a group of sequentially connected
spin systems will still cause the whole group to be appropriately
assigned.
    * In Assignment -> Resonances: Added ability to edit shift values, but
only if a shift is not associated with any peaks in the specified shift
list. Added another column for, and the ability to view, peaks that are
connected to a resonance in the selected shift list only.
    * Shift Match Distance Constraints: Spectrum NOE working chemical
shift ranges are now remembered.
    * Constraints: Added check for repeated resonances (usually diagonal
peaks) when making constraints from peak lists.
    * In Assignment -> Assignment Panel: Added the option to remove the
atom or spin system assignment of a peak-linked resonance.