List of changes in release
Changes from 2014 Mar 27 (2.4.0) to 2014 Oct 03 (2.4.1) release
-
Added optional MolSystem column in Assignment Panel suggested resonance
table.
-
Added way to show strips for resonances in a single residue, most useful
for two orthogonal views in 3D (or higher) windows, along with a 2D
window, in the Resonances browser. (Functionality originally implemented
by Igor Barsukov back in Analysis v1.)
-
New Structure --> Cyana menu (instead of having to run a macro).
Changes from 2013 Jun 12 (2.3.0) to 2014 Mar 27 (2.4.0) release
-
Fully integrated running of CYANA calculations with read-back of results, via macros
in the module macros/MultiStructure.
-
Ctrl + left mouse drag in spectrum window prints out basic region stats (sum, average,
standard deviation) for the spectra in that region.
-
Added executive summary for project (Project --> Summary).
-
Add Peak Normalisation in Structure --> Make Distance Restraints dialog
Changes from 2012 Feb 29 (2.2.2) to 2013 Jun 12 (2.3.0) release
-
Added CPMG fitting (but probably needs more work).
-
Added C - A exp(-Bx) fitting.
-
Added interface to D2D (http://www-vendruscolo.ch.cam.ac.uk/d2D/index.php).
-
Added interface to CamCoil (http://www-vendruscolo.ch.cam.ac.uk/camcoil.php)
Changes from 2010 Oct 04 (2.2.0) to 2012 Feb 29 (2.2.2) release
-
Added new type nomenclature for MAS solid state and 13C direct detection experiments, this also
affects 'NOESY' experiment types which become 'through-space'.
-
Allow the generation of many more synthetic peak lists with more options: Can now generate peak lists
for HNcoCA, HNcoCACB and almost all MAS solid state experiment types. There is a new option to control
the number of bonds for 'through-space' transfers (when not using a structure).
-
When calculating distances for structures with multiple models 1/r^3 ensemble averaging is now used.
-
Added a new experiment series type for CPMG pulsing frequency.
-
Added double quantum experiment types with corresponding DQ window axes, multi-position DQ
cross-hairs, and automatic extraction of component chemical shifts during assignment, e.g. as
displayed in the Atom Browser.
-
Allow the loading of structures that represent only sub-sequences of a current molecular system.
-
Added trial module to draw T1, T2, Het NOE relaxation analysis graphs (note that this will be replaced
with Mark Howard's module for version 3).
-
Added Guy Montelione's and Janet Huang's RPF functionality (Recall, Precision, F-measure; as used in
AutoStructure) to the structure menu. This is a new "PyRPF" implementation. The objective here is to
compare through-space peak lists with sort distances in a structure to find 'missing' peaks and
'unexplained' peaks. This allows for an overall estimation of a validation score and in this Python
implementation provides a mechanism for the user to quickly zoom to points in the spectra where the
peak list and structure are not consistent.
-
Added CCPN user registration system.
-
Added automatic bug reporting system.
-
The Ramachandran plot has been adjusted so that the allowed/disallowed regions etc. better match with
the original PROCHECK categories.
-
Added MakeDecoupledPeakList macro, i.e. to get rid of all splittings and to show the underlying main
resonance locations.
-
Added lots and lots of new functionality based upon non-uniform isotopic labelling of molecules. The
user can use a standard, pure labelling scheme or create 'labelled molecules' (recommended) by
associating a scheme (or mixture of schemes, or segmental labelling, or a modified scheme) with a
given set of experiments. Using the latter method will mean that labelling is automatically considered
when doing assignments, making restraints, making synthetic peak lists etc.
-
Added extra spinning sideband diagonals for MAS spectra when the spinning frequency is set for the
experiment.
-
Added ability to change relaxation fudge factor in 3J HHa coupling measurement.
-
Added the interface to launch ARIA into the Structure menu.
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Distance restraints may now be generated for indirect through-space experiments like Ch_hC.NOESY; in
which case the restrained atoms are not actually observed in the experiment.
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Structure import records the original coordinate file name in model details.
Changes from 2010 Aug 12 (2.1.5) to 2010 Oct 04 (2.2.0) release
-
Improved 3J HHa coupling extraction system:
Added ability to change relaxation correction factor.
The GUI now plots the measured couplings on a Karplus curve.
-
Added graphical interfaces to control external programs:
* PALES, MARS & MODULE2; require separate installation)
* MECCANO; we distribute the C code but the user must compile the code (and also install GSL, the GNU Scientific Library)
-
Added back the show struct connections for unassigned dimensionss of through-space peaks
-
Added deletion of measurements within measurement lists; except for shifts that
are still assigned to peaks
-
Lots of new functionality to handle 13C double quantum experiments:
* Added the C[DQ(CC)] experiment type
* Spectrum windows can be made with a 13C DQ axis type: totally distinct
from normal 13C axis
* Window crosshairs and marks automatically display the related DQ
locations
* Assingment augmented so that the DQ components can be assigned
independently
* DQ assignments contribute to chemical shifts in the proper, per
component manner.
-
Added Molecule:Isotope Labelling functionality:
* The user can setup the labelled versions of molecules that appear in an
experimental sample
* Each sample can potentially be a mixuture of multiple labelling patterns
* A labelling patern is easily created from an existing isotopomer scheme
* Mixed scheme 'chimeric' residue patterns may be created
* Labelling patterns may be manually adjusted; per isotopomer and per atom
levels
* All previous functionality that used isotopomer schemes can now also use
the new patterns
* Labelling can (if setup) be deduced automatically by virtue if an
experiment being in a sample
Added GUI for doing ARIA structure calculations:
* Can interface with a locally installed ARIA GUI
* Can be run remotely on CCPN Grid
* We can give out grid service passwords on request
* CCPN Grid is non-commercial use only (unless CNS licensed)
-
Added a prototype relaxaion analysis module:
* Available at python/ccpnmr/analysis/macros/RelaxationAnalysis.py
* Plots T1 vs T2 with S2 & Tau_m lines
* plots T1/T2 vs sequence
* Plots T1, T2, NOE vs sequence
* No documentation yet
* Model free estimation of S2 will be incorporated in due course
-
Added the ability to make distance restraints from indirect through space
experiments:
* For example Ch_hC.NOESY where 13C is detected by transfer is between 1H
* Using an indirect experiment like this allows bond length errors to be
added to distances
* Some experiment types for solid state are currently missing
-
The protein backbone sequence assignment tool can now use input spectra with any
dimension ordering (in the past the HNcoCA HNCA etc had to match).
-
Swapping prochiral resonances for prochiral methyls will now swap both linked H
and C (should the swap make sense with regards to experiment dimension onebond
relationships)
-
The geometry of all popup windows is checked to make sure that at load time the
always appear within the screen bounds.
-
Changes from 2010 Feb 16 (2.1.3) to 2010 Aug 12 (2.1.5) release
-
Added tool-tips and in-program documentation
-
Added Bayes peak separator functionality
-
Simplified experiment type setting using classification sub-menus and common types
-
Print window dialog extended so that you can specify which spectra and peaks
are drawn, independently of what is shown on the screen, and you can now
specify the tick font and spacing, and specify the scaling in terms of
cms or inches per unit (or unit per cms or inches) instead of in terms
of percentage.
-
Added HADDOCK, for macromolecular docking on remote server, to main Analysis
Structure menu
-
Added functionality to extract diffusion coefficients from DOSY pesudo-2D data,
including gradient strength NMR series and Aexp(-Bx^2) fitting
-
Added check for seq assignment system if linked spin systems go through proline or
fall off edge of sequence
-
Added Find Reciprocal Peaks (return peaks) button to NOE Contributions system
-
Added concentration units for Kd calculation
-
Added creation of co-linearity restraints to H-bond generation
-
Added FixProchiralSwaps macro: to separate prochirals with two distinct shifts if
they get mixed up
-
Added sequence page-wrapping, changable fonts and greyed-out unassigned residues
for secondary structure chart
-
Added Show Peaks and Show Restraint funtions for violations
-
Added "Synthetic?" column for peak list table
-
Added whole-ensemble RMSD
-
Editing of experiment reference dimensions & transfers simplified: A<->B rather
than A->B, B->A
-
Stripping peaks now done in strip axis ppm order
-
If you display strips in a window and it is closed then it will be opened
Changes from 2009 Nov 11 (2.1.2) to 2010 Feb 16 (2.1.3) release
-
Area selection in windows now uses stippling instead of just a rectangle.
-
Non-contour window popups that are open are now remembered, including their
location, when the project is saved.
-
Added Kd calculation, which includes "binding site" concentration field.
-
Added isotope labelling scheme and intra-residue filter to synthetic peak list
creation
-
Added macro (python/ccpnmr/analysis/macros/) to set B factor slots from shift
difference lists - a hack for display purposes
-
Fix for Cys disulphide links messing with quality reports
-
DANGLE now has slightly faster execution
-
Added ability to introduce callbacks for opening/closing/saving projects.
Changes from 2009 Sep 16 (2.1.0) to 2009 Nov 11 (2.1.2) release
-
Added info message for resonance split.
-
Added Selected Resonances table; accessed from various parts of Analysis.
This gives a table of just a subset of resonances, e.g. for a peak or spin system
-
Added Resonance Info table; accessed from various parts of Analysis. Gives a table
of a resonances shifts and the peak dims to which it is assigned. Very useful for
finding outliers
-
Lots of significant Analysis GUI rearrangements; button renamings, menu renamings,
menu shuffle, menu icons...
-
Changed Spin system typing Monte-Carlo search to proper Metropolis-Hastings and
nested sampling
-
Added 1.2 multiplier and 20 number of levels to edit contours
-
When making synthetic peaks from structure, you can now specify a minimum peak
intensity and duplicate peaks are avoided
-
Added ability to save shift differences as shift difference lists
-
MARS automatic backbone assignment is integrated and ready, subject to approval
by the author
-
When generating distance restraints you can now filter possibilities by cutting
off large distances according to a guide structure (e.g. model or earlier ARIA run).
-
Added positive/negative contour toggle to top of spectrum window (in Contours option)
-
We now allow specification of shift list and molecular system when making synthetic
peaks from shifts; before it used what was set else where for the selected experiment.
-
In the chemical compound table the locally available entries are now coloured
differently
-
Change to peak annotations where {a}[b] [c] [d] can now become {a}[b] [c] {a}[d]
where appropriate.
-
Fix to remove spin system type cache, which was not updated. It is now quicker anyhow.
-
When linking sequential spin systems there is now a choice of total peak score or
average peak score to rank the matches; total is the default.
-
Network anchoring reworked to make it work for solid state data
-
Crosshair is now tracked in Reference Chemical Shift Popup simulataneously with
spectrum windows.
-
Changes from 2009 Apr 06 (2.0.7) to 2009 Sep 16 (2.1.0) release
- 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.
Changes from 2009 Jan 27 (2.0.6) to 2009 Apr 06 (2.0.7) release
- Added structure validation option to Structure menu. Calls CING remotely via the
iCing server in Nijmegen.
- Added trial version of the Entry Completion Interface for preparing BMRB/PDB
depositions. We will give details how to avtivate upon request.
- Increased the number of types of spectra that you can create synthetic peak lists
for. This includes HNCO, HNCA, HNCACB, HNHA, HN_H.TOCSY, HN_H.NOESY. The rule is
that the there must be a direct transfer between the measured experimental
dimensions. This excludes for example HNcoCA where transfers via the CO is not
represented by an experimental dimension.
- Added "Propagate Merit" option to the peak tables. This allows easy en masse setting
of a peak worthiness. Good for resurrecting disgruntled ARIA peaks.
- Added calculation and display of peak line widths via peak tables (but still doesn't
deal with overlap too well).
- In Restraints & Violations, added funtion to split a restraint list in two according
to whether restraints are violated or not violated.
- Added "Process All" option to Link NOEs, to assign a whole peak list. Use with
caution.
- Improved file selector, with more space, file history, navigation buttons etc.
- Added new check to Quality Reports: Warn if only one prochiral of an atom pair is
assigned to a peak dimension if the other prochiral is very close in chemical shift.
- Synthetic peaks are now down-weighted (0.01) in the chemical shift calculation.
- Added automatic tidy of unused dataLocations when spectra are deleted.
- Added button in Edit Structures to remove residue validation parameters. (e.g.
RMSDs).
- Added ability to focus on selected residue in Edit Structures.
- Structures are no longer selected by default in the Restraints tab. (This could be
very slow). Updating of the restraints table now made faster, including when
calculating structural values is enables.
- Improvements to the Nexus automatic sequence assignment: It copes better with bad
data, and the scores in the graph are now unlikely to give spuriously high scores.
The scores are now based on both rate of convergence and goodness of sequential
matches.
- Display or spin system strips now takes an optional shift list setting.
- Added isotope labelling hilighting to the Assignment Graph.
- Added setting of minimum isotope fraction in Edit Assignment popup (only used with a
labelling scheme).
- Generating peaks from Restraints improved: Was missing some hetero atom assignments
before.
- Can now generate restraints for carbon-carbon through-space transfer experiments.
- Isotope labelling filtering of assignment options now works for resonances that have
a residue type and atom type but no sequence number.
- Added "frequency" and "pulsing frequency" to NMR series condition types.
- Added some functionality for 1D shapes.
- Make importing Bruker spectra easier by allowing selection of proc files several
directories up.
- Various bug fixes dealing with sampled dimensions in spectra.
Changes from 2008 Oct 17 (2.0.5) to 2009 Jan 27 (2.0.6) release
- Make main menu names consistent with title of popups where possible.
- Windows menu now lists the windows in an order dependent on isotopes.
- Much wider use of Greek unicode characters in the user interface.
- Disabled the ability to click and pick peaks outside the contour regions.
- Added double click to activate strip.
- Spin system popup has been split into tabs.
- Carobhydrate stereochemistries are now listed as alpha or beta.
- When setting spectrum contour colours the colours are now listed
by hue.
- Fix loading of large (>= 2GB) spectrum data files.
Changes from 2008 Oct 14 (2.0.4) to 2008 Oct 17 (2.0.5) release
- Just a bug fix: loading projects didn't work.
Changes from 2007 Jul 12 (1.0.15) to 2008 Oct 14 (2.0.4) release
- In LinkPeakLists, 3D windows are no longer mandatory for navigating in 2Ds.
- Added ability to load PDB files for missing residues. Ability to work with structure ensembles throughout Analysis.
- Addeded ChemicalShifts table for PostScript generation, etc.
- Added DANGLE (dihedral angle and secondary structure prediction based on chemical shifts)
- Old default CCPN macros now removed and replaced by options in assignment menu.
- Added editing of isotope labelling schemes. Added isotope labelling schemes to restraint generation, atom browser and predicting peaks from structures.
- Re-organisation of main menus.
- Unification of popups by using tabs.
- Added the ability to display RMSD and residue validation results on a structure.
- Added the ability to setup spectrometers and instruments, with which experiments were run.
- Added Nexus, an automatic backbone assignment routine.
- Linking sequential spin systems can now use 1H-correlation spectra.
- Added user profiles.
- Negative contour levels can be set separately from positive levels now.
- Added ability to update existing distance restraints in light of new peak assignments.
- Secondary chemical shifts now use sequence-dependent adjustments.
- In violation analysis added the proportion of ensemble violated, and colour coded accordingly.
- When importing PDB structures, the PDB chain codes and sequences are preserved where possible.
- Added Greek unicode characters to atom browser.
- Added ability to work with through space peak lists other than NOESY, eg. solid state experiments.
- Format Converter threading defaults to off when launched from Analysis.
- Added ability to customise residue codes via profiles.
- Added ability to load and describe reduced dimensionality / projection spectra.
- Clicking on the structure viewer highlights the names of the selected residue.
- Analysis code re-organised into subdirectories.
- Added icons for help, close and the new popup function, clone (which makes a new popup of the same sort).
- Added ability to quickly add a sequence without having to go through all the complicated setup.
- Added residue tab to Edit Structure popup. This displays phi/psi angles, RMSDs, validation results, etc.
- When precisely placing peaks in pseudo-3Ds, they are displayed in all visible planes.
- Spin system typing much faster now.
- Big revamp of Ramachandran plot and NOE matrix plot.
Changes from 2007 Apr 10 (1.0.14) to 2007 Jul 02 (1.0.15) release
- Changed spectrum shortcut keys from numbers to F keys.
- Allow Bruker and NmrPipe data to be pseudo-ND.
- Extended font setting to ScrolledMatrix and Tkinter.Frame
- Matching shifts for assignment and making restraints is now sensitive to
the appropriate molSystem.
- Peaks with figOfMerit == 0, are no longer used in chem shift calculation.
- Added export of rates intensities and params from CalcRatesPopup.
- Added optional SEGIDs to ARIA export.
- Added ability to make peaks in arbitrary NOE spectrum from distance constraint list.
- User can now specify initial chain and mol system codes.
- Disabled unlocking of molecules until further notice.
- Added "All Residues" and "Spin Systems" to atom assignment summary.
- Added more and optional delta (to random coil) shift opts in the secondary structure
graph popup.
Changes from 2007 Jan 22 (1.0.13) to 2007 Apr 10 (1.0.14) release
- Added functionality for displaying 1D spectra (but lots still needs to be
done). In the Window --> New Window dialog these are obtained by selecting
the y axis to be of type 'value'.
- There is now an option to have 2-char shortcuts. This can be selected
in the Other -> General Options dialog (the last checkbutton option). The
way 2-char shortcuts work is that if there is a 1-char shortcut that matches
the first character typed then that will be run, otherwise it will run the
2-char shortcut when the second character is typed (if there is a matching
one).
- There is a new way to re-reference a spectrum by aligning a peak from
that spectrum on top of a peak from anoter spectrum. You first select the
peak whose spectrum you want to re-reference and then select the peak which
it should be aligned to in the fixed spectrum. With these two peaks selected,
and the mouse over the fixed peak, you then choose the right mouse menu
Peak --> Re-reference to this peak option, which brings up a dialog which
lets you change the referencing.
- With the Window --> Print Window dialog you can now specfiy exact regions
to print (rather than what you see on the screen). To do this select the
"Use override region when printing" option.
- Added ability to ambiguate prochiral resonances.
- Addition of functionality for slow exchange and Lagmuir curve fitting.
- Data Analysis --> Rates Analysis now copes with 'num delays' series.
- Allow selection of a reference plane in a pseudo-3D, which won't be used in
fitting.
- Added option to go to the previous group when calculating rates and following
shifts.
- User can edit initial molecular system and chain codes.
- Added first version of popup to efficiently link NOE peaks to existing resonances
given shift and structure information.
- Changes to allow some control of which windows a spectrum is mapped into upon load.
- Added clear connections button in structure viewer. Fixed refresh after dist method
change.
- Added 'Scrollbars' and 'Crosshair traces' options to mouse menu.
- Added z1,z2 region scrolling with middle mouse wheel plus ctrl/shift/alt.
Changes from 2006 Nov 15 (1.0.12) release to 2007 Jan 22 (1.0.13) release
- Allow setting of peak font and whether or not peak pointer is drawn. This
is specified by spectrum and can be set in the Experiment --> Edit Spectra
dialog.
- Allow 1D slice to be drawn on crosshair. This is specified by window
and by spectrum. So a slice is drawn for a spectrum if and only if slices
are allowed to be drawn for the window and for that spectrum. Whether a
slice can be drawn for a window is specified in the Window --> Edit Window
dialog (int the fourth and fifth columns of the top table), and whether it
can be drawn for a given spectrum in that window is specified in the
Window --> Mapped Spectra dialog (in the next to last column of the top table).
The Tk implementation uses xor'ing to draw the slice and the OpenGL one does
not, so the appearance is different.
- Put in check and warning for duplicate experiment names.
- Disallow having 0 maxMarks and maxRulers.
- When cloning a spectrumWindow also copy the spectrumWindowView properties.
- In 1D slices when scaling up and down, scale relative to 0, not relative
to center of canvas.
- Make standard message dialogs center on current popup rather than center
of screen.
- Add timestamp mechanism so that Analysis does not have to initialise
certain information if the data was last updated by Analysis rather than
some other program.
- Added for Windows systems.
- The upgrade mechanism should now automatically recompile C code if that
is required.
Changes from 2006 Aug 02 (1.0.11) release to 2006 Nov 15 (1.0.12) release
- Updated Analysis to deal with new and forthcoming changes to the data model.
In particular all data model packages now have top objects. There is also a new
package for HADDOCK projects.
- Added the ability to create stored (precalculated) contour files. This is
useful if disk space or speed (because of memory) is an issue. (Before now all
contours were calculated on-the-fly.) This is available from the Experiment
-> Edit Spectra dialog, with the "Contour Files" button.
- Added the ability to move peak annotations (labels). With a peak selected,
you press 'q' and the annotation will move to the location pointed to by the
mouse cursor.
- Added functions and menu options for auto peak label arranging ('w' is the
keyboard shortcut), and resetting to the default.
- Added a pointer from the peak annotation (label) to the peak center if they
are far enough apart.
- Added 1D window slice options to the window section of the right mouse menu.
- Added a confirmation upon peak list deletion.
- When viewing constraints, added annotation '*' for fixedResonances that
represent more than normal atoms sets (e.g. whole residue in HADDOCK)
- Added attempt to resolve prochirals (doesn't deal with ensembles yet) for
violation estimation
- Added better quick peak annotations where there are multiple chain codes.
- Added functions to create a transpose peak list from an existing one.
This is accessible from the Crosspeaks -> Current Peak Lists dialog.
- Spectrum window strips can now be horizontal instead of vertical (the default).
- Added intra-residue filter option in the edit assignment popup.
- Added a system macro to remove all marks and rulers - takes the 'n' key shortcut.
- Added more options for displaying nucleotides in the atom browser, so that you
can display base and sugar atoms on separate rows.
- Added option and popup to follow shift changes, e.g. during titrations or temperature
series.
- Added option to deassign a given dimension number of the selected peaks, in the
Crosspeaks -> Edit Peak List dialog.
- Added option to only use assigned peaks when calculating the reference NOE intensity.
- Added option to use NOE sum or min dist for calculating the structural value for
distance constraints, and when displaying distances on the structure viewer.
- Added propagation of experiment type to selection in top table of the Experiment ->
Experiment Types dialog.
- Added options to create synthetic peaklists. These include synthetic NOEs from
a structure, a peaklist using shifts from correlated resonances (e.g. make 2D 13C-HSQC
from higher dimensionality assignments), and a function to make a transposed peaklist
from an existing one.
- Rates analysis can now be done using pseudo-3D data files from Azara.
Correspondingly the experiment series dialog has been upgraded so that it can deal
with either separate experiments per sample or with pseudo-3D experiments (where one
dimension is sampled).
- Change to give peak dimensions for sampled data an annotation.
- Added use of ButtonScrollbar to change orthogonal view of sampled (non-frequency)
dimensions.
- Changed default display of strip midpoints and strip numbers to on.
- Changed Window -> New Window dialog so that you can choose which spectra will be
displayed (and appear in the toolbar) before the window opens.
- In the structure viewer there are changes to enable display of distances between
whole atom sets rather than giving connections between every possible atom pair.
- Code migration for *Basic modules. Mostly adding findFirstObjects(), sortedObjects()
and new package heads (top objects).
- Displaying spin system strips now works with bound resonances even if they're not in
the same spin system. (Esp. important for N-CO)
- Obtaining NOE distances from peak intensities is now done in a generalised manner
using an r^-6 curve (although bins still exist).
- First version of Network anchoring module.
- Windows should pan and zoom more smoothly with the mouse
Changes from 2006 Apr 10 (1.0.10) release to 2006 Aug 02 (1.0.11) release
- Added browsAtomsMacro - Goes in for the 'b' key as a system macro.
- Allow ambiguous peakDim anotations e.g. "(4Ala/6Ala)CA([123]/[456])" if
there are two contribs
- Added function to find constraints given selected peaks in ConstraintBrowser.
- Added option to remove resonances from peaks after deassigning resonance in ResonanceBrowser.
- Merge botton now does Merge/Split depending on selection, in ResonanceBrowser.
- Added in NOE dist function manipulation for constraint generation including network anchoring.
- Added storage of preferred NOE intensity type by spectrum.
- Aria1.* export uses constraint serial rather than peak serial.
- Testing shift matching distance constraints now lists peaks with poor merit
- Added getNoeDistance() in ConstraintBasic to do the d = k / r^6
- Added attempt to resolve prochirals (not ensembles yet) for violation
estimation
- CalcAmbigDistConstraints now works with 4D and higher NOESYs. Bonded dims
no longer passed-in - now deduced from experiment type.
- Fix for loading structures with imperfect residue mappings, e.g.
smaller -> larger num residues.
- Added atom type check (from BMRB data) when assigning resonances.
- First version of Network anchoring module. Not for anonymous assignments
at present.
- Added options and functions to find symmetry related peaks.
- First versions of assignment report and quality control apparatus.
- Added CSI v2 file reading.
- Prochiral distance measurements now non zero.
- Changed default display of strip midpoints and numbers to on.
- Added "2 to 4 residues" option in AssignmentGraph.
- Added option to read NmrView data files (courtesy of Gary Thompson of the
University of Leeds) and Bruker data files.
- Changed orthogonal dimension j/k shortcuts so that they work on strip
where cursor is rather than on active one.
- Using ctrl drag middle mouse button you can now zoom into a specified
region.
- Put extra padding of half a point in orthogonal dimensions for peak
viewing and selection.
- Fixed bug in rates analysis error estimates (some variables were not
being initialised to 0).
- In Rates Analysis popup add option to use bootstrap method for calculation
of the TC error estimate (the default) or to use the previous (pre 1.0.9
Analysis) method.
Changes from 2006 Feb 03 (1.0.9) release to 2006 Apr 10 (1.0.10) release
- Experiment series now use sample conditions. This change should be
simple but note that sample conditions essentially belong to experiments
and persist independently of experiment series. The condition type has
changed from "Time" to "delay time".
- Make top module long and thin by removing Quit and Help buttons.
- Added option to clone windows in Window -> Edit Window.
- Added option to allow contour levels to be separated additively rather
- Added option to run Python script on Analysis startup, by defining
ANALYSIS_STARTUP environment variable similar to the normal Python
PYTHONSTARTUP environment variable.
- Added memory logging under Project menu. (Counts Python objects which
have not been garbage collected.)
- Move Version from Project to new Help menu. Add About and Help to
Help menu.
- Allow peaks to be "snapped" to local extremum (if for some reason they
have been moved away from this local extremum). It uses the boxWidth of
either the peak or the spectrum (the latter can be set in the dialog
Crosspeaks -> Peak Find Parameters) to determine how far to search, and
the peak is moved if and only if there is exactly one extremum in that box.
This is available either as a keyboard shortcut (P by default) or under the
right mouse menu Peak.
- Added new option to main menu under Molecule, called Copy Chain Assignments.
You can use this popup to either transfer or duplicate residue assignments
between similar chains. This popup has the option to copy on a per residue
basis. Also, if duplicating assignments, the peak assignments can also be
duplicated
- In the Assignment menu added Link Seq Spin Systems. This popup enables
you to setup search and query spectra for matching peak positions, e.g. as
used to do sequential C backbone assignments. In this case potential
sequential spin systems are displayed as strips. A selected spin system
can be linked sequentially, and appropriate resonances, spin system
groupings, etc., are automatically made.
- Analysis now prints warning to the command shell if it finds proton
resonances which are bound to more than one other resonance, according
to atomic assignments and peak assignments, given 1-bond transfers.
- Added a macro to AssignmentMacros to initialise HNCO or HNCOCA peak
lists in the same manner as initialiseHSQC.
- The resonance browser now sets atom type for multiply selected
resonances.
- The constraint browser now does a violation analysis for distance and
dihedral constraints, given a structure. Also, there is the ability to
jump to the peak assignment table with a single click, assuming the
constraint is only derived from one peak.
- Added the ability to merge constraint lists, and also split constraint
lists, according to ambiguous or unambiguous (pro-chirals don't count as
ambiguous).
- Added the ability to display dihedral constaints on the structures.
- Increased the number of window navigation options (under the right
mouse menu Navigate), including 3D to 2D and similar.
- Added the ability to import constraints, violations and structures
from an Aria2 run directory.
- The EditAssignment popup resets scrollbar positions when the peak is
changed. The new resonance button has been created which replaces the
option in the right-hand tables. Added molecule system filtering option.
Correlated dimensions option replaces bound resonances and repeated
spin system options. This new option uses the reference experiment
information.
- For the peak tables (selected and whole peak list) added a button
to put marks through selected peaks.
- Expanded the resonance browser with various navigation and marking
options, similar to Igor Barsukov's macro.
- The LinkPeakLists popup now remembers settings (when project is
saved). It also allows you to specify the maximum number of marks to
use.
- The CopyPeakAssignments popup now uses a distance threshold that
is weighted according to isotope.
- Generally, NOE distances do now use r to the -6 averaging.
- Can now move the active strip left and right using the buttons
at the top in the strip bar of the graphics window.
- Added mouse wheel zooming of spectra, and scrolling of tables.
- You can now calculate shift differences for unassigned resonances.
Changes from 2005 Dec 22 (1.0.8) release to 2006 Feb 03 (1.0.9) release
- New popup added called "link peaklists" which can be used to connect
a root spectrum (e.g. HSQC) to other related spectra. You can pick the
other spectra based on the root positions, assign the root resonances
and also assign non-root resonances for the appropriate spectra. This
popup replaces the pickAssignSpecFromRoot and assign3DTocsyF2NewResonances
macros, but allows the user to link window navigation to perform these
operations on an individual spin system basis. Documentation for this
is missing for now.
- API and related molecule creation bugs fixed so that storage isModified
attribute set correctly, so that saveModified() does indeed save modified
data.
- Changed rate constant error estimate method (to a "bootstrap" method).
- The heteronuclear NOE list generation now includes an error estimate.
- For ambiguous prochirals such as Val gamma and Leu delta the a or b
label is consistent between the C and the H.
- Notifiers have been changed so that Analysis doesn't do as much work
if a popup is closed.
- The "find close peaks" option now allows selection of the spectra.
- Assigning spin system sequential connectivity into loops is not
possible now.
- Structure loading is more robust and quicker.
- Can load structures which are subsets of the chain sequence.
- You can deassign peaks from the Edit PeakList popup now.
- Macro loading can now detect functions with a space between the name
and the left parenthesis.
- For window navigation functions, notifiers have been added for changing
windows so they are now refreshed correctly.
- Several fixes for the "match peak" option. (This was ignoring certain
peak lists in certain circumstances.)
- For the "match peaks" popup, rulers are now optional. The root
assignment is displayed and more window options are given.
- An "options" choice has been added to the marker right mouse menu.
- The copy peak assignments popup has an option to assign only singly
matched targets.
Changes from 2005 Oct 27 (1.0.7) release to 2005 Dec 22 (1.0.8) release
- Lots of bug fixes.
- Modified installation script to better allow use of OSX Framework glut.
- Added a module UserSpectrum, so that users can create new spectra. This
also lets you write data to the (new) data file.
- Added a new module Data Analysis -> Shift Differences. Allows
comparisons of pairs of shifts between peaks in two peakLists. Useful,
for example, for working out changes in an HSQC.
- Hand-picked peaks (using ctrl-shift) no longer have their centers
fitted (using parabolic interpolation).
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
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:
- 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
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.