Changes from 2005 Oct 11 (1.0.6) release to 2005 Oct 27 (1.0.7) release

• Assignment --> Secondary Struc Chart is now available to display sequential and medium-range NOE information, carbon shift differences and secondary structure. This will be extended to include 3JHnHa, H/D exchange and CSI at a later date.
• In the graphics windows, the peaks toggle frame has a new option at the left, "Multi-list". If this is on (the default) then more than one peak list can be active in the window, otherwise only one is.
• Exp transfers are automatically being set for experiments that have a reference experiment.
• Random coil chemical shift values are now in the reference data (not visible in the GUI, of interest to programmers).

Changes from 2005 Aug 12 (1.0.5) release to 2005 Oct 11 (1.0.6) release

• 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 refers 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:
  • 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.
  • 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.

Changes from 2005 Jun 27 (1.0.4) release to 2005 Aug 12 (1.0.5) release

• Make sure that at least one plane drawn in orthogonal dimensions.
• There is a new mouse mode for selecting peaks in spectrum windows: Left Click + Drag - This selects peaks in a given region, but the selection is not additive, i.e. all other peaks are deselected. The original additive mode is still available with Left Click + + Drag.
• For the copy peak assignments popup the follow peaks option now works for possible target peaks as well as the source peaks.
• Residue and chain columns have been added for the measurements browser. This means that for measurements such as T1 you can plot the value against residue number using the graphing options.
• The macro pickAssignSpecFrom2dRoot (which is loaded by default) has been superseded by pickAssignSpecFromRoot which is much more flexible in terms of dimensionality and isotopes. The only condition for picking and assigning a spectrum based on the positions of peaks in the root spectrum is that all of the root dimensions must match different dimensions in the target (in terms of isotope). Thus the root can be of the same or lesser dimensionality. For any target dimension which doesn't match the root the whole spectral width is used, i.e. you can use an HSQC to pick 'columns' of an HQSC-NOESY. The macro is located in the module python/ccpnmr/analysis/macros/AssignmentBasic.py
• The active peak list for a spectrum can now also be set in Crosspeaks::Current Peak Lists.
• There's a bug fix for the HeteroNOE calculation popup. Changing the intensity type between 'height' and 'volume' now updates the intensity ratios in the table.
• Deassigning and reassigning some spin system residues was causing annotation problems. For example, sometimes a Gly residue would end up with two 'Haa' resonances. This is now fixed.
• In the resonance browser the option to delete orphans works differently: Only shifts are deleted for resonances not connected to any peaks (of the current shift list). If deleting a shift results in a resonance with no shifts at all then the user has the option to delete the resonance too.
• When fitting functions to peak intensities, e.g. for T1 rate analysis, a new error is now given. This error is the error in the time constant (or equivalent) of the fitted function. It is separate from the fit error which measures the goodness-of-fit of the function to the data. The time constant error takes into account both the error in the peak intensities (defaults to spectrum noise level) and the error in the time points (set via experiment series). It is calculated by randomly sampling function fits within the errors of the data points, and thus varies slightly upon recalculation. Note that Analysis does not yet have the option to manually set peak intensity errors, but this will appear in a future version.
• PeakList cloning was not working when the destination peakList did not have the same spectrum as the source peakList. This has been fixed.
• If you delete the activePeakList for a spectrum then the activePeakList now defaults to the last peakList for the spectrum.
• Find/Goto Peak functions now works with the active strip.

Changes from 2005 May 24 (1.0.3) release to 2005 Jun 27 (1.0.4) release

• Fixed parabolic fit volume so does not just return infinity.
• Allow optional -m argument at program startup, which specifies graphics memory usage in megabytes (default 64).
• Spectra are now drawn in inverse order (as determined by the Order column in Experiment -> Edit Spectra), so the lowest order ones are drawn last and so appear on top.
• Make "box sum" the default peak volume method (as set in Crosspeaks -> Peak Find Parameters), instead of "parabolic fit".
• Change orthogonal scrolling so that clicking on arrows moves either a tenth of the bubble size (the previous rule) or the minimum plane size (over all the spectra mapped onto the window), whichever is greater.
• Fix C code bug which meant freeing of cache could cause crash.
• In ccp.api.Molecule.MolResidue seqId has been removed, it has been replaced by serial as the key and seqCode to hold what used to be the seqId.
• Moved various funtions from Util to WindowBasic and ExperimentBasic.
• More documentation which was missing last time has been included.
• For many popups: Make sure that only active windows being considered.
• Added parent for dialogs. Was sometimes not visible otherwise for some reason.
• Bug fix for calculating shift value standard deviations for spectra with non-unary weightings.
• In EditAssignment dialog added 'Bound resonances' and 'Double tolerances' options, and added [Merge F%d Resonances] and [Show All Peaks] buttons.
• In ExperimentBasic added 'rb' flag when opening data file in isDataBigEndian(), because otherwise does not work on Windows platforms.
• In SpinSystemTyping enabled selection of different shift lists.
• In StructureBasic small fix for when the number of residues in chains and structures don't match.
• Fixed sign error bug in peak finding with diagonal exclusion.

Changes from 2005 Mar 11 (1.0.2) release to 2005 May 24 (1.0.3) release

• 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).

• 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.

• 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.

• 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).

• The message ticker has been removed for now (it was causing problems in some circumstances because Tcl/Tk is not thread safe).
• 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.

Changes from 2004 Dec 15 (1.0.1) release to 2005 Mar 11 (1.0.2) release

• The Analysis code can now be compiled without OpenGL/glut. And even if the code is compiled with OpenGL/glut, the user can choose Tk instead of OpenGL for the graphics windows at runtime, by selecting the menu Other -> General Options and setting the Graphics Handler to Tk (this will be the only choice if Analysis has not been compiled with OpenGL/glut).
• There is now a simpler way of changing the project details in the "save as" popup. This should mean that normally the user does not have to worry about the details of URLs, Storages, etc.
• EditStructurePopup now displays the structure.
• ViewStructurePopup is new, this is the popup which displays structures, constraints and peak connections. This is driven from several parts of Analysis, for example, you can display individual constraints from constraint lists, peak connections from peaks in the selected peaks (via right mouse menu) or in a peak list. And you can also display potential assignment possibilities on the structure. Thus many of the other popups now have a structure pulldown menu.
• You can print these structures to file (in PostScript, not quite in Pdf yet).
• The right mouse menu on the graphics windows has been tidied up. Most noticeably the assignment functions have been separated from the peak functions.
• In EditPeakListPopup if you have a structure selected and there are two H dimensions for the peaks a H-H distance column will appear. This is useful for plotting distances versus peak intensity.
• The top part of the graphics windows now have a scrollbar so that all the information can be viewed even if the window is narrow. (It also means that when you re-open a project the window stays narrow if it was saved to be narrow.)
• You can copy peak lists in two different ways now, in EditPeakListsPopup. One way is to clone the peaks exactly. The other is to reproduce the peaks, i.e. to re-pick them using the peak finding algorithm.
• You can now set fonts in Analysis under Other -> Fonts.
• ScrolledMatrix tables can have a font set individually (only temporary, not remembered if you quit the Project and then open again).
• Spin system sequential connectivity (i-1, i+1, etc.) has been added to EditSpinSystemPopup, and to the right mouse menu. For example, in the right mouse menu you can say whether the spin systems that relate to the peak dimensions are i, i-1, i for an HNCOCA experiment. In EditSpinSystemPopup you can add spin systems to sequentially connected chains in the Seq. Segment column. Assigning one spin system to a residue in a connected series will propagate the assignments to the rest if compatible.
• In BrowseConstraintsPopup there is a button called Setup Resonances, which can be used to generate resonances that you can assign to from an imported constraint list which doesn't link to any known resonances.
• In the python/ccpnmr/analysis directory there is now a macros subdirectory. This is a new home for Analysis macros. To start off with this contains AssignmentMacros.py, TutorialMacros.py (which was used in the teaching course -- these macros will be fully documented on the website soon) and, courtesy of Magnus Helgstrand, CopyAssMacro.py which transfers assignments between separate peak lists.
• The documentation has not quite kept up with all these changes.

Changes from 2004 Nov 23 (last 1.0 beta) release to 2004 Dec 15 (first 1.0) release

• Fixed bug when printing windows (to PostScript or PDF) which meant contours were often coming out in wrong location and with wrong aspect ratio. Also added some code which means that strip plot windows will print out correctly in PostScript now (not in PDF because of clipping, which is still to be implemented). Also PDF now does black and white (as opposed to colour) output. (But possibly still some problems with PDF in landscape mode.)
• Can now make intra-molecule disulphide links when you make a molecule.
• ResidueInfoPopup now displays a 3D picture of the residue (with idealised coordinates), as does EditSmallMoleculePopup.
• The Assignment panel has an extra option to restrict resonance possibilities to those which are in repeated residues or spin systems, e.g. useful when assigning HSQCs.
• Bizarre system-specified colors for popups have been defaulted to grey.
• Merge resonances is fixed (shifts were not merged previously).
• The help buttons now have documentation.
• Copy peak lists now much quicker and just clones the list.
• Atom browser assignment status is now much more robust. HB*, etc., will only be assigned if stereospecific options are assigned.
• Deleting a color deletes similarly named color scheme.
• Fixed the DNA/RNA three letter codes for odd phosphorylation states.
• When you make a distance constraint list it does not automatically display the constraints any more since this might take a long time. Viewing of tables of constraints is much much (an order of magnitude) faster.
• When editing entries in a table the focus does not disappear when the cursor leaves that field (although the cursor must remain on the table).
• Unaliasing a peak now checks to see if the new position is inside the current spectrum bounds and if not the user may extend the bounds of the spectrum.
• Bugs in setting the sequence of chain fragments (in molecular systems) are fixed.
• Reference chemical shift distributions now have reversed ppm axis.
• Deleting a window axis does not delete entire window now.
• When generating distance constraints the user is warned of any peaks which do not have an intensity.
• Importing and matching structures to existing chains works better.
• Graphical windows now have a help button (in top right corner).

Changes from 2004 Oct 20 release to 2004 Nov 23 release

• Lots of documentation has been added. It is in the doc sub-directory of analysis.
• First release with strip plots in properly. In right-mouse menu there is strip option to add and remove strips in a window and to move strips between windows. Also there is a toggle at the top of the graphics windows to control the active strip (for orthogonal dimension scrolling) and to add and remove strips. The active strip is the one for which "goto position" works.
• In right-mouse menu in peaks option there is a new match peak groups function. This operates on the currently selected peaks and will try to match other groups of peaks in a specified spectrum and dimension. For example, you can use this to find candidates for the sequence neighbours of a residue from noesy peaks, etc.
• Scrolled graph, which for example is used to view BMRB chemical shift distributions, is undergoing a re-write. Currently this means that the global coordinates are displayed for the cursor position, and a crosshair is drawn.
• In EditPeaksPopup and SelectedPeaksPopup the follow peaks option (which was a mode) has been changed to a button.
• There is now an option to extend contour tiling to cover unaliased peaks, i.e. the minAliasedFreq and maxAliasedFreq for a spectrum are adjusted automatically (on startup and when you create/move a peak) to be large enough to include all 'real resonance'/unaliased peak positions. This option is set to ON by default, but you can switch it OFF in Main Menu::Other::General Options Also the minAliasedFreq and maxAliasedFreq for a spectrum may still be manually set via Main Menu::Experiment::Edit Spectra.[Referencing]

Changes from 2004 Oct 08 release to 2004 Oct 20 release

• Put horizontal and vertical separators back in. These allow multiple views on a window and will hopefully be used for strip plots (so different than the current awkward system).
• Allow propagate peak assignments to be spread across peaks from different spectra. Uses isotopes as the key.
• Shift match distance constraints has had bug fixes and the chemical shift ranges are now set for each dimension.
• Various window wobbling problems have been fixed.
• New right mouse menu option Peak -> Propagate peak's unaliasing which will give selected peaks the same unaliasing as the current peak (under the mouse).

Changes from 2004 Aug 26 release to 2004 Oct 08 release

• Rename xml files when saving project as extra backup.
• Add box in graphics windows showing fundamental region of spectra.
• In some ScrolledMatrix tables, for example, the Peak List Editor, you can now select multiple rows, using shift key for extending for ctrl key for toggling.
• In ScrolledMatrix tables, sorting has been changed for strings with numbers at the start, e.g. 1A comes before 10.
• You can now open multiple spectra at once.
• If verification dialogs skipped when opening spectra then the endianess of the data is guessed.
• Experiments have links to molecular systems, and this is automatically set when a peak within an experiment is assigned to a particular molecular system.
• The molecular system setup has been changed to display chain fragments and to make chains based upon molecule templates. These templates are created and modified in a separate popup, Molecule -> Molecule Templates. The latter lets you create templates by incorporating stretches of polymer and other small molecules. Provision to link these together will be added in future. This popup also displays derived information for the molecule, e.g. molecular mass and empirical formula. For a molecule template without a chain you can change the amino acid type and protonation state of the residues.
• The atom browser has colouring according to the chemical element. Options have been added to remove all assignments from a particular atom mapping (the resonances themselves still exist). There is an option to show the peaks involved in a particular assignment.
• The edit assignment popup (Assignment -> Assignment Panel) has an option to display resonance possibilities plus or minus N spectral widths away if you think the peak might be aliased. Assigning to such resonances is visible by colours and will automatically cause the peak dimension to be unaliased (with warning). The option to create a new resonance has been coloured green.
• Rates analysis has been tested and fixed.
• Shift-matched distance constraints now has an option to test shift match before committing to generating the constraints. This test indicates which peaks fail to match for various reasons.
• In the graphics windows, the scrolling of the top widgets has been restricted to the part showing the spectra, peak lists, etc. "Goto position" replaces "goto orthogonal". This now gives more options as you now need only one equivalent dimension in target window.
• There was a speed-up for loading projects associated with peak annotations.
• There is now a ticker message in the top-level popup giving some information.
• Prochiral methyls now have the non-stereospecific options available. Backwards compatibility is an issue, atom set mappings will need to be remade, instructions can be given upon request.

Changes from 2004 Aug 13 release to 2004 Aug 26 release

• Clouds options now available under Other menu: so far 'Relaxation Matrix Optimisation', 'Proton Molecular Dynamics' and 'Filter Clouds'.
• In ScrolledMatrix (table) widgets can now use arrow keys and Home, End, PageUp and PageDown keys to navigate.
• In resonance browser can now view resonances with isotope code unknown.

Changes from 2004 Aug 10 release to 2004 Aug 13 release

• FormatConverter changed so that now does not change stdout, so should work properly embedded inside Analysis.
• Modified peak volume calculation (but still not great).
• Add Recalculate Intensities button in the EditPeakListPopup and SelectPeakPopup dialogs.

Changes from 2004 Jul 02 release to 2004 Aug 10 release

• Added 'depth' cueing for peaks, so that peaks get lighter the further they are from the cental plane.
• Aliased peaks are now drawn with dashed rather than solid lines.
• Added Version onto Project menu, so can find program version from graphical interface (it's also mentioned at start-up).
• Added Strip Group functionality (still basic).
• There is now provision for multiple shift lists. When you open a spectrum, or edit an experiment, you can specify shift list.
• The ability to make covalent links has been removed for now.
• Rates analysis to measure T1, T2, etc., has been added. This includes grouping of peaks in different spectra and various fitting functions (linear, log-linear, nonlinear).
• In Data analysis -> Measurements you can now recalculate shift values.
• The import of Felix data had a bug which swapped refpt and refppm and got the latter in the wrong units (Hz instead of ppm).
• In the right-mouse menu for Peak there is now 'Make intermediate peak' which puts a peak at the average of a group of peaks.
• In the right-mouse menu for Peak the option 'Find close peaks' now sorts by delta.
• Moved to NmrConstraints package (new in data model) so that constraints are now stored in separate XML file.
• Added getCurrentWindowPopup() to argServer (for macros).

Changes from 2004 Jun 23 release to 2004 Jul 02 release

• The location of the dialog popups is now remembered in between runs. (Up to now only the graphics windows had their screen locations remembered.)
• In scrolled matrices (tables) any two numerical columns can be plotted one against the other. This is accessible from the right mouse menu.
• Scrolled matrices (tables) can be output in PostScript. This is accessible from the right mouse menu.
• A macro submenu has been added to the right mouse menu. Macros can be added to this submenu via the Macros -> Edit Macros dialog. Any macros that are run can make use of the cursor position, closest peak, etc, via new argServer functions: getCurrentPeak(), getCurrentWindow(), getCurrentSpectra(), getCurrentPeakLists(), getCurrentPosition().
• If a macro fails to load the real Python error is now passed forward so that you can see exactly where anything may be wrong in the code. Also macros that are invalid/broken can now be removed easily from the project.
• Spectrum data dimension chemical shift weighting has been added which may be useful if you have a spectrum with broad/imprecise peaks that you don't want to infulence shift vaules, or if you're automatically assigning a NOESY and you don't want any guessed peaks to have an effect. The weights can be set in Experiment --> Edit Spectra using the Tolerances dialog.
• Assigning directly to ambigous mappings is now functional (this necessarily involes the addition of an extra resonance to a peakDim). If non-sterospecific pair of resonances exist and one is susequently assigned stereospecifically then the other in the pair becomes the other sterospecific option. E.g. for Hba, Hbb when Hba changes to Hb3, Hbb automatically becomes Hb2. If you assign a resonance to atom type only then any existing or subsequent spin system assignment will cause the resonance to be fully assigned if the atom type is appropriate for the residue. For prochiral pairs the 'a' label is always the upfield resonance. This adjusts automatically according to the existance and position of the other resonance.

Changes from 2004 Jun 05 release to 2004 Jun 23 release

• Added popup to set the NOE->constraint distance mapping classes. Stored on a per spectrum basis.
• Added ability to calculate distance conatrants from the assigned peaks of an NOE peak list.
• Added popup to generate potentially ambiguous distance constraints for incompletely assigned NOE peaks by chemical shift matching. With provision for peak aliasing, selection of particular molecules and chemical shift ranges. Similar to AZARA connect.
• Spectrum windows: added, to the right-mouse menu, a function to center the orthogonal, z planes of a window on a given peak, so that it is in the middle of the depth selection.
• Added global option to display molecular system information on peak annotations and also resonance naming (gui only, not resonance.name).
• Added a funtion in MoleculeBasic to move a molecular chain between different molsystems. Note that this funtion is highly illegal because it uses mergeObjects(), which bypasses the API. Use at your own risk. However, the function may prove useful if the initial mol system set-up was wrong for an advanced project.
• Added functions to find/identify covalently bound resonances.
• Better handling of anonymous amino acid X - now used for all unresolvable three- and one-letter codes.
• Copy polymer function added to EditMolSystemsPopup - useful for homooligomers.
• Can now assign resonances to atom type only via atom browser.
• Constraint list browser now views/manipulates individual ambiguous items. Also, just as a stop-gap, lists can be exported to ARIA .tbl files.
• Added new assignment macros, which are included by default in new projects: pickAssignSpecFrom2dRoot will pick peaks in 3d spectra according to a picked 2d root and assign these peaks to the same resonances and spin systems. assign3dTocsyF2NewResonances assigns new resonances to the F2 dimensions of 3d TOCSY peaks.
• Added provision for setting aromatic ring resonance equivalency globally at chain creation time, and on an individual residue basis via BrowseAtomsPopup.

Changes from 2004 May 25 release to 2004 Jun 05 release

• Fixed it so that quitting before having saved new project brings up same dialogue as "save as" (otherwise the API complained about directories not existing).
• Added some explicit OpenGL flushing (seems to be done implicitly by Mesa but not by some other OpenGL implementations).
• Rearranged initialisation of OpenGL so that Mac OSX version does not crash when drawing graphical windows.
• Added NOE Matrix display (under Assignment menu).

Changes from 2004 Mar 26 release to 2004 May 25 release

• Added merit score for peaks (entered by hand currently).
• Allow minimal annotation for peaks (to reduce screen clutter).
• Graphics windows now have toggling peak lists.

Changes from 2004 Feb 26 release to 2004 Mar 26 release

• Added message at start-up giving release information.
• Fixed bug which meant that the C initialisation for peak lists was not always happening.
• Removed mouse modes. Now to find peaks in a region you need to hold shift and ctrl key down while dragging cursor.
• Removed general options from main dialog and put in its own dialog under Other --> General Options.
• Changed temporary license expiry date from 31 March 2004 to 31 December 2004.
• Added ability to specify center of xy region by double clicking on coordinates label in top frame of graphical windows.
• In Data Analysis menu there is a Calculate Hetero NOE option which pops up a dialog which allows you to make a heteronuclear NOE list which then appears as a measurement list.
• In the right mouse click Peak submenu there is now ability to find close peaks.
• Added Experiment Series module under Experiment menu, which allows series of experiments to be set up for which some parameter varies.

Changes from 2004 Jan 30 release to 2004 Feb 26 release

• Added check on byte order when loading spectra.
• Incorporated spectrum menu into experiment menu and added various experiment dialogs: ability to edit and view experiments and experimental parameters, to view measurement lists and measurements.
• Experiments can change shift lists.
• On right mouse click the assign menu has become the peak menu, and within the peak menu have ability to clear peak assignments, add the assigned resonances to a particular spin system, and peaks can be unaliased.
• There is a new Residue Information popup on the molecules menu, which gives the sequential context of different residue types and their assignment status.
• In the Peak Draw Parameters popup (on the peaks menu) you can now change the annotation used when drawing peaks.

Changes from 2004 Jan 15 release to 2004 Jan 30 release

• Upgrade to Mesa 6.0 from Mesa 4.0.

Changes from 2003 Dec 05 release to 2004 Jan 15 release

• Added panning with up/down/left/right arrow keys.
• Added auto-backup facility.
• Fixed bug which caused PS/PDF output not to finish.
• Allowed 'params' as keyword in Azara par files (value just ignored).
• Added peak drawing size options (the default being uniform number of pixels).
• Propagate appropriate assignments across selected peaks.
• Some more options on right mouse menu (e.g. goto orthogonal plane).
• Peak and resonance annotations carry spin system information where appropriate.
• Reference chemical shifts now show multiple distributions per residue type.
• Fixed mutex locking bug which meant that window froze after awhile.
• Fixed scrollbar and tick sizing bug which meant that on start-up window had to be at least a certain size.

Changes from 2003 Nov 14 release to 2003 Dec 05 release

• Various bug fixes.

Changes from 2003 Oct 23 release to 2003 Nov 14 release

• Fixed bug which meant that window peak list symbols and annotation were not being turned on and off correctly.
• Improved speed of the loading up of projects (most noticeable for projects with lots of peaks).
• Added Structure to top-level menu. Allows import of PDB files. Can view coordinates (as text). Used to show distances in assignment procedure.
• Assignment procedures modified, e.g. you can now choose possibilities for all the dimensions at once.
• There is now reference chemical shift data (sourced from the BMRB) viewable under the Molecules menu.

Changes from 2003 Sep 26 release to 2003 Oct 23 release

• Fix minor bugs in EditPeakPopup.
• Fix aliasing bug in PeakBasic and WindowDraw (points start at 1, not 0).
• Switch middle mouse zoom behaviour so that up is now in and down out.
• Fix bug in PrintWindow which meant that contours were not coming out in the correct location in hardcopy output.

Changes from 2003 Sep 11 release to 2003 Sep 26 release

• Re-work atom browser dialog.
• Add General Editor option on Other menu, which allows a generic visual editing of API objects.

Changes from 2003 Sep 05 release to 2003 Sep 11 release

• When opening spectrum for which a new window is created, instead of creating orthogonal dimensions to be a tenth of the world region, make them one plane at the midpoint of the spectrum, and when a new window is created using NewWindowPopup make orthogonal dimensions a hundredth instead of a tenth of the world region.
• Add X11 flags into C makefiles (in case not on system path).
• Change OpenSpectrumPopup dialog so that no longer have "as left" experiment option. Either type name in by hand or choose name from existing experiments.
• Fix UCSF reader to use correct bytes for determining nucleus.
• Add diagonal in spectrum windows with equal x, y axis types.