Hello,

There are now new releases, 1.0.8 for the FormatConverter and 1.0.6 for
Analysis.  Wim can tell you about the FormatConverter changes.  For
Analysis changes, see the long list at the bottom (and there are probably
things we forgot to mention there).

The main really important thing to note is that from this release we are
shipping Python 2.4 instead of Python 2.2.  The reason we made this change
is that most of are using Python 2.4 (the rest on 2.3) and sooner or later
some non-Python-2.2 feature is going to creep in by mistake (this already
happened once in a relatively trivial case).  And there are some 2.3/2.4
features we want to use now (such as booleans really being boolean).  In
fact there is already one 2.3 feature in the code to do with how text
files are opened (fortunately 2.2 silently ignores the 2.3-ness).  For the
next release or two we'll try to avoid relying on non-2.2 features but
assume that sooner or later you should all upgrade to 2.4.  (In theory the
general Python performance is supposed to be much better in these newer
releases, so that in itself is a good reason to upgrade.)

The other thing Analysis users will notice with this new release is that
you will be asked to specify a reference experiment for each experiment
(for both existing experiments and any new you create).  There is not yet
much functionality in Analysis to use this information but looking forward
it's obviously going to be helpful for assignment.  There is a library of
reference experiments that is shipped with Analysis (and the
FormatConverter).  Suggestions are welcome on how this works and whether
anything should be added or modified.

And Analysis also has an update feature which should allow bug fixes to be
grabbed from our server in between releases.  Tim will explain more about
that in another email.

Wayne

**************************************************************

CHANGES:

    * Make Python 2.4 the version which is shipped.
    * There is now a converter for NMRPipe to Azara data formats. The
reason we need this is because NMRPipe data is not blocked and that makes
contouring very slow. For now the script is in
ccpnmr1.0/python/ccpnmr/analysis and is called NmrPipeData.py. To run it
you type "python NmrPipeData.py" and follow the instructions.
    * Make Tk the default graphics handler instead of OpenGL (but you can
still choose OpenGL; this is set in Other -> General Options -> Graphics
Handler).
    * Allow (most of) right-mouse menu to be accessed via keyboard. The
key "u" pops up the menu (the "u" can be changed by the user via the
Macros --> Edit Macros dialog). The "escape" key pops down the menu. You
can navigate inside the menu using the keyboard shortcuts shown in the
menu items.
    * Add some shortcuts: 'j' for scrolling left in z1 (the first
orthogonal dimension); 'k' for scrolling right in z1; 'i' for increasing
the number of contours for the active spectra in a window; 'o' for
decreasing the number of contours; 'e' for moving the contour levels up
for the active spectra in a window; 'r' for moving the contour levels
down.
    * New CcpNmr Software Update functionality under the Project -->
Upgrade menu. Analysis now has a new system to provide file updates
between major releases. Most bug fixed files will be posted on a server
which can be queried for upgrades. The upgrades can be installed only if
the user has write permission to the CcpNmr installation directories.
    * New Edit Experiment Type Popup functionality under the Experiment
--> Experiment Types menu. This allows the user to link experiments to
reference experiments and thus specify the class of experiment in terms of
magnetistion transfer, atom sites, measurements etc. If the user has an
existing project with no reference experiments specified then the user
will be prompted to set the ref experiment types. Otherwise the linking of
reference experiment is only prompted at load time, but may be altered at
any time via the Experiment menu.
    * Peak Selection Popup and Edit Peak List Popup changes. Added [Make
strips] - Makes strips in a window based on the positions of the peaks
selected in the table. Added [Strip locations] this will make strips in
vairous windows, including various orthogonal options, based upon peaks
selected in the table. This is especially useful for making strips in a 3D
window based upon peaks in a 2D spectrum: e.g. You can sort an HSQC by
residue then plot sequential spin systems as strips in a 3D window to look
at sequential connectivity. The volume method is now listed in one of the
columns.
    * Edit Peak List Popup changes. For the peak "Status" filtering
pulldown, an "Intra Spin System" option has been added.
    * Atom Browser changes. You can now select a shift list so that the
assignment status, as indicated by the darkening of atom selections, only
referes to one shift list. There is also the option to ignore shift list
info which displays things the same as previous versions.
    * Browse Constraints Popup changes. You can now specify a structure to
which constraint distances are compared to.
    * Generate Constraints Popup changes. There is now an option to choose
between two different ways of getting a constraint distance from an NOE
peak intensity. The first, as before divides the peak intensity by the
peak list average and looks up a distance class in a table. The second
option "Normalised" makes a couple of simple of corrections before doing
the distance lookup. These are:
          o For 15N HSQC-NOESY peaks the intra residue Hn-Ha peak is
scaled to be of average peak list intensity - i.e within the bin for 2.8
A, and all of the other peaks for the same amide are scaled by the same
amount.
          o For all NOEs, the peak intensity is scaled by the number of
protons represented by each of the resonances - mostly important for
methyls.
      The primary reason for this option is CLOUDS. There is also a
[Calculate ADCs] option which is used to generate non-NOE/anti-distance
constraints for 2D NOESYs. This is really only for the CLOUDS protocol.
    * Confirm Sequential Spin Systems Popup changes. This popup has been
created in anticipation of dealing with the spin system connectivity
information obtained from automated backbone assignment programs.
    * Edit Spin Systems Popup changes. The [Display Strips] option now
works on multiple spin systems selected from the table.
    * Scrolled Matrix changes. The ScrolledMatrix tables can now make
graphs using columns of data that contain strings provided there are
numerals at the beginning of the string entries. This is especially useful
for graphing residue numbers which are in strings of the the form
'11Ala','12Glu','13Phe' etc.
    * Stand Alone Application Template. Located at
$CCPN_HOME/python/memops/editor/ApplicationTemplate.py this code provides
a basis for creating new appilcation programs. It is separate from the
CcpNmr applications but has the ability of dealing with CCPN projects
(load, save, backup etc)and provides a basis for a menu. Also, this
project launches PopupTemplate.py. to start this type "python -i
ApplicationTemplate.py".
    * Popup Template - gui examples. Located at
$CCPN_HOME/python/editor/PopupTemplate.py this popup is a demonstration of
many of the graphical widgets available within CCPN to create new
applications and macros. This code definitely needs more explanatory code,
but for now should serve as an example of how to use the various GUI
components.
    * Increase default memory for C cache from 64 to 128 megabytes.