Enhancements and bug fixes introduced in each Sparky version are listed below.
May 30, 2008
|Project file paths
||Fixed bug where incorrect paths to spectrum session files are put into
a project file. Happened when Sparky is started from a shell in a project
directory with a project file specified on the command-line. Saving the
project then puts incorrect paths (extra "../") in the project file.
Problem did not occur with files opened with the File menu, or with full
file paths specified on the command-line.
July 12, 2007
||Made Sparky work on Windows Vista. Sparky 3.113 did not start on Vista.
Worked after updating Python 2.4.2 to 2.5.1 and Tcl/Tk from 8.4.12 to 8.4.14.
October 13, 2006
||Fixed problem where spectrum views from strip plots appeared in the
Sparky Windows menu. The menu entries were never removed even if strips
were closed and selecting one would cause a crash.
|Fonts too small
||Some extension dialogs containing lists using fixed-width fonts used
incredibly small default fonts (3 or 4 points) on Linux. Changed code to
always use 12 point font.
||Fixed pipe2ucsf segmentation fault that happened when converting
projected spectra when axis 3 (or 4) was not projected.
||Incorporated changes to atom name translation file atomnames.py
submitted by Eiso AB.
Feb 8, 2006
||Fixed problem where assigning dozens of new resonances in the presence
of hundreds of already assigned resonances caused crash on Windows and high
CPU use on Linux. Caused by resonance menu memory leak.
||Updated from Python 2.3.3 to Python 2.4.2.
||Updated from Tcl/Tk 8.4.5 to Tcl/Tk 8.4.12.
||Fixed bug where deleted fit line caused incorrect display of fit curves.
A fit curve for the wrong peak would be shown.
||Fixed exception that is raised when trying to display assignment lines for
an unassigned 3D peak.
Added code so that selecting assigned peak in 3D spectrum tries to draw line
in Chimera between 1H atoms. Formerly, only peaks selected in 2D spectra
||Fixed bug that made peak table list lines contain curly brackets,
and table saving fail.
Added new start line pattern for reading chemical shifts from AutoAssign.
Needed because of slightly changed header line (extra space at end) in
latest AutoAssign (April 27, 2005).
March 22, 2005
||Fixed problem on Windows where Sparky did not start if spaces were in
the installation path.
Feb 25, 2004
||Packaged Mac version as a Mac application with an icon that can be
placed on desktop or in dock. Still requires X windows.
||Made Sparky install at any location without having to edit startup script.
||Changed method for showing manual pages in web browser when Help buttons
pressed. Now tries to use default browser on Windows and Mac, Mozilla on
Linux and Netscape on other machines. Can be changed using SHOW_URL_COMMAND
environment variable in startup script on unix systems.
||Updated from Python 2.1 to Python 2.3.3. Including Python with Sparky
distributions now instead of requiring separate download.
||Updated from Tcl/Tk 8.3.4 to 8.4.5.
||Added option for relaxation fitting to use peak volumes instead of heights.
||Added spectrum menu to ornament sizes dialog. It now acts on the
chosen spectrum instead of the spectrum having selected ornaments.
||Fixed several extensions that did not work correctly with peak groups
because they could not get peak height.
|Spin graph assigner
||Fixed bug where proposed assignments involving peak groups caused a
Python exception. Made pattern axes menus in setup dialog only show
choices that are consistent with spectrum nucleus types.
||Updated example Python extension in manual so it works again.
Feb 21, 2003
||Allowed use of shifted peak markers in each spectrum in relaxation fitting.
||Put in support for reading spectrum files larger than 2 gigabytes
on some platforms.
July 31, 2002
||Added abilitiy to set pointer mode in Python and get notifications
that pointer mode changed.
||Made code comply better with ANSI C++ standard.
February 19, 2002
||Fixed bug where pipe2ucsf produced peak positions off by 1 data point
||Added specific error messages when command-line arguments are bad.
January 21, 2002
|Removed license verification||Took out code checks trial licenses.
||Improved compilation instructions and included readme-code.html
describing the source code for developers.
December 18, 2001
||Switched from Python 1.5.2 to Python 2.1.1. Also upgraded from
Tcl/Tk 8.0.5 to Tcl/Tk 8.3.4.
|Mac OS X version
||Compiled Sparky on Mac OS 10.1 with X server.
||Updated Sparky interface to molecular graphics program Chimera to
work with latest Chimera.
November 12, 2001
|Spaces in path bug
||Fixed bug where spaces in path to NMR data or Sparky session files
caused loading data to fail.
|Peak assignment labels
||Added commands to add (lb) or remove (lB) assignment labels from
October 9, 2001
||Can change spectrum and view names used in menus with the
spectrum settings dialog (st).
|Renumber view command
||Change a spectrum view name to use the lowest available
suffix number with the renumber view command rv. If only one view of
a spectrum exists then it will have no suffix number. This
allows you to get rid of the pesky "/1" in "noesy_100ms/1" if you only
have one view.
|Printing 4D spectra
||Fixed a bug that produced illegal Postscript when printing a 4D spectrum.
August 28, 2001
|Spectrum region RMSD
||Added command (rm) to show mean and rmsd values for a spectrum
region selected with the mouse.
|Python region selection notice
||Added region selection notice to Python interface.
Provides callback when user drags a box in a spectrum with the mouse.
|Crash when quitting
||Fixed a bug that caused core dump when quitting.
Happened when a Python extension registered a callback
with the C++ Sparky module.
June 14, 2001
||Added "write peak lists" and "read shifts" buttons so Sparky interface
can be used while running AutoAssign manually with its native interface.
||Fixed bug in spectrum overlay dialog where pressing remove button always
removed first overlay in list instead of the selected overlay.
||Allowed choosing multiple overlays in spectrum overlay dialog for removing
more than one overlay at a time.
|Peak delete bug
||Fixed bug where selecting a peak, pressing mouse button on it, hitting
delete, and then lifting mouse button caused Sparky to crash.
June 6, 2001
||Made strip plot vertical scrollbar allow scrolling to cover strip with
largest ppm range.
||Made destroying warning dialog invoke a default choice.
||Added initialization in Peak constructor for mFitResidual.
|Python peak volume
||Made peak volume, volume_method, and fit_height python attributes settable.
Feb 15, 2001
||Fixed file is smaller than expected error message to show correct file
and expected sizes.
|Duplicate save files
||Fixed bug that occured if project contained save file twice.
Spectrum would be unloaded leaving view creation parameters pointing
to deleted spectrum.
||Made move button move partially assigned peaks.
|Contour redraw bug
||Added code to work around a gcc 2.95.2 PC linux compiler bug that
caused the same tile to be continuously redrawn.
Added comments about 80 bit Intel x86 FPU problems.
||Made slice not update if pointer just moves along current slice.
Made slices update when z-plane changes.
||Fixed bug where spectrum data memory cache immediately freed large
spectrum blocks right after they are allocated. Locked element being
added to cache so it can not be freed in the add_to_cache() call.
Dec 12, 2000
||Added interface to specify sweepwidths in spectrum settings dialog (st).
Made peak alias commands use new spectrum sweepwidth parameter.
Made resonance panel aliasing use new spectrum sweep_width parameter.
Added sweep_width attribute to Python Spectrum class which can differ from
spectrum width. Updated Python extensions to use sweep_width for aliasing.
||Fixed bug undoing peak delete after spectrum has been closed.
||Made selecting atom with no expected peaks not produce an error.
||Added assignments to new peaks and checked for already existing assigned
||Fixed HNCACO expected peaks to include both i and i-1 CO.
||Added program matrix2ucsf to convert an array of floats to a UCSF format
|Z plane step
||Added zu, zd commands to move downfield or upfield one plane.
|AutoAssign on Windows
||Noted in manual that AutoAssign interface does not work under Windows.
Unable to use fork() to start AutoAssign server and client.
||Cleaned up add selected peak strips code.
|Memory allocation fix
||Made new request for 0 bytes return non-zero pointer.
|Chimera molecule view
||Fixed bug where selection handler was registered many times.
Fixed undefined references to chimera.
|Read peak list
||Recognize lower case atom names (h, c, n) in splitting group from atom.
Changed split_group_atom() in sputil.py to allow lower case atom names.
||Eliminated unused and broken warn() routine.
July 14, 2000
Changes before this release not recorded.
Dates for some earlier releases
|3.91||May 1 2000
|3.87||Mar 3 2000
|3.85||Feb 29 2000
|3.76||Nov 15 1999
|3.74||Oct 21 1999
|3.72||Oct 14 1999
|3.66||Mar 4 1999
|3.64||Jan 26 1999
|3.62||Nov 17 1998
|3.58||Sep 14 1998
|3.37||Nov 18 1997
|3.21||Jun 24 1997
|3.3||Mar 3 1997