added:
2022
- July 2022
- **UPDATE** <a href=http://wiki.cara.nmr.ch/StructureCalculationWithAtnosCandid">!DSSref</a> AU script for calibration of Topspin spectra was updated to remove halfpixel correction, which was needed for old Topspin versions.
2021
- July 2021<br>
- **UPDATE** <a href="AllCaluaScripts#MarkScriptsToExportFileForAProgram">!WriteAssignments.lua</a> Updated to support writing out shifts in BMRB NMRSTAR 3.1 format
News on CARA and wiki updates are posted here (Latest at top)
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2022
- July 2022
- UPDATE DSSref AU script for calibration of Topspin spectra was updated to remove halfpixel correction, which was needed for old Topspin versions.
2021
2019
2018
- April 2018
- March 2018
- NEW TEMPLATE ProteinLiquidState1.9v1.cara was added to the CARA templates page. It is the standard template for assignment of proteins in the liquid state.
- It features:
- new atoms allowing assignment of exchangeable Ser and Thr hydroxyls
- new SpectrumTypes to represent 2D projections of 3D spectra
- nearly all CALUA scripts have been updated.
- It replaces:
- ProteinLiquidState1.3v9.cara Released Oct. 01, 2013 (Last Updated: Oct. 01 2013) (Version 9)
- This deprecated template was intended for assignment of 1H, 15N, and 13C/15N-labeled proteins using liquid state NMR spectra with CARA 1.8.4 and upwards authored by F. Damberger and was compatible with BMRB nomenclature. The BMRB statistics were from bmrb on June, 25, 2010. It was based upon the Start1.3v8.cara. Compared to this previous template, the BBresidue ResidueType was modified to allow picking of HA2 and HA3 in GLY spin-systems during analysis of triple resonance spectra HBHA(CO)NH and HBHANH. A number of the included LUA scripts were updated.
2017
2016
- September 2016
- Additions to wiki tutorials on working with automated NOESY assignment and structure calculation
- NEW ReadCyanaPeakList.lua reads peaklists generated by CYANA which include ambiguous (multiple) assignments
- UPDATE PeakListNumberedByResidue.lua added option to use alias shifts of a spectrum
- UPDATE WriteAssignments.lua can write out RNA/DNA assignments
- August 2016
- wiki information was generally updated (e.g. links to Forum replaced those to the defunct blog)
- LUA pages were updated. To simplify maintainance and make it easier to find scripts, the many LUA script pages were merged into a single page with navigation index at the top.
- A number of standard LUA scripts were updated:
- CopyProjectedSpinsToOriginSystem.lua
- CreateOriginSystemsFromProjectedSpins.lua
- LoadBmrbStatistics.lua
- RecalibrateSpectra.lua
- ShiftSpinsInCatagory.lua)
2015
- September 2015
- A new stable release 1.9.0 is available from the download site. This release adds functionality to the LUA commands to import spectra into projects and allows spectra which are not found during loading of the repository to be ignored. See release notes for details.
- A beta release of CARA 1.9.1b18 includes support for larger spectra (64 bit) and a new scope for analysis of 4D spectra. It also supports relative pathnames for spectra.
- NEW LUA script ChemShiftMapFromTwoPeakLists.lua to generate chemical shift mapping data from two peaklists.
- Updated LUA script CopyAssignmentsToProject.lua to fix bugs and add option to copy only spins within a specified SpinId range
- NEW LUA script CompareProjects.lua to compare the assignments in two projects and report differences (assigned in only one, signficant shift deviations)
- Updated LUA script WriteSparkyPeakList.lua so it can write 2D, 3D, and 4D sparky peaklists.
- Updated LUA script UplsToSpinLinks.lua, Pseudoatom names QQ,Q are converted to IUPAC, expands pseudoatoms in UPLs? when both assignments are in project, allows spinlink color to be set
- beta release 1.9.0b18. Continued development of 4Dscope. Introduces 2nd cursor for comparing intensities of peaks in orthogonal plane. Set cursor with "0" and release with "00". Toggle 4D plane in left with "4". Revised handling of inferred peaks in NOESY spectra.
- NEW ChemShiftMapFromTwoPeakLists.lua script for generating chemical shift mapping data from two peaklists.
- August 2015
- beta releases of 1.9.0b13 through 1.9.0b17.
- Continued development of 4Dscope
- Development of new software architecture for CARA
- revisions to new LUA binding
- Running with Qt 4.8.
- New debugger with callbacks, stack, local variable views and disassembler for LUA binaries.
- LUA terminal is accesible during Debug breaks (expressions available, no assignments or calls permitted)
- LUA editor supports long comments and strings
- Scaling of spectra according to Topspins NC_proc parameter introduced starting with 1.9.0b16
- June 2015
- Updated CopyAssignmentsToProject.lua script to fix bugs and add option to copy only spins within a specified SpinId range
- NEW CompareProjects.lua script to compare the assignments in two projects and report differences (assigned in only one, signficant shift deviations)
- Updated WriteSparkyPeakList.lua so it can write 2D, 3D, and 4D sparky peaklists.
- Updated LUA script UplsToSpinLinks.lua, Pseudoatom names QQ,Q are converted to IUPAC, expands pseudoatoms in UPLs? when both assignments are in project, allows spinlink color to be set
- March 2015
- New CARA beta release 1.9.1b12 incorporating a new scope for analysing 4D spectra.
2014
- September 2014
- Updated LUA script CopyProjectedSpinsToOriginSystem.lua to introduce the option to overwrite shifts of origin spins (e.g. CA) with shifts from projected spins (e.g. CA-1)
- Added new LUA script GetLineWidthsFromPeakLists.lua which writes peaknumber;linewidth to a file for each peak in a peaklist along the selected dimension of a spectrum
2013
- October 2013
- Updated CARA template for assigning proteins with liquid state NMR (ProteinLiquidState1.3v9.cara, derived from Start1.3v8.cara), and solid state sNMR spectra (ProteinSolidState1.0v2.cara) on the TemplatesPage. Both templates were modified so that GLY HA2 and HA3 are accessible during assignment of HBHA(CO)NH and HBHANH triple resonance spectra by changing the generic SpinSystem BBresidue. A number of the included LUA scripts were also updated.
- Updated CARA template for assigning nucleic acids with liquid state NMR (NucleicAcids1.2.cara, derived from NucleicAcids1.1v1.cara) on the TemplatesPage.
- February 2013
- New CARA stable release 1.9.0 based on the 1.9.0b9 (see below).
- New CARA beta release 1.9.0b9. Includes changes to LUA commands for importing spectra allowing the spectra to be assigned a name. Issues in 1.9.0b8 causing data loss during import of repositories generated with older CARA versions were fixed.
home attribute of pos tag was retired. All peaks now inherit the homeSpectrum of their PeakList. If spectra are missing (not located at the pathname specified by the repository when it is opened) they can be ignored. They appear in the SpectrumExplorer as grey entries that are struck out. These will be reactivated, if the spectra are present at the specified pathname when the repository is opened.
- Updated CARA template for assigning proteins with solid state NMR spectra ProteinSolidState1.0v2.cara on the TemplatesPage
- January 2013
- Release new CARA template for assigning proteins with solid state sNMR spectra ProteinSolidState1.0v1.cara on the TemplatesPage
- New CARA beta release 1.9.0b8. Includes changes to LUA commands for importing spectra allowing the spectra to be assigned a name. Issues causing crashes under certain circumstances during the import of spectra with LUA scripts have been fixed.
2012
- November 2012
- Due to memory management issues, Issue tracker access was changed. To add issues or search latest issues apply for a login with the CDT. You can access an archive of the tracker from Nov. 30. 2012 here.
- September 2012
- New CARA beta release 1.9.0b7. Includes experimental alpha release of LUA adaptor for NLopt?.
2011
- December 2011
- WriteTalosFile.lua has been updated to fix bugs and write out TALOS+ format. Numbering is by ChainNr?.
2010
- January 2010
- The site www.nmr.ch was expanded to serve the interests of the swiss nmr community. The link to the CARA software site can be found under the catagory Swiss NMR software.
- New CARA beta release 1.9.0b2.
- Release of new version of template: Start1.3v8.cara available on the TemplatesPage
- Release of new template for nucleic acids: NucleicAcid1.1v1.cara on the TemplatesPage
- CopySpinSystemsAndAssignmentsToAnotherProject.lua has been added to the script collection. It facilitates the merging of data from different projects.
2009
- November 2009
- CARA wiki and tracker move to new addresses
- August 2009
- CorrectAtomMagnitudes.lua has been added to the script collection. It sets all methyl atom magnitudes to 3 correcting an error in the standard template Start1.2.cara
- WriteInputForMars.lua has been added to the script collection. It writes out the chemical shift assignments for the systems in a format suitable for backbone assignment with MARS.
- SparkyAssignmentsToCara.lua has been added to the script collection. It imports the chemical shift assignments from a Sparky assignment list file into a CARA project.
- WriteSparkyPeakList.lua has been added to the script collection. It writes out a peaklist in sparky format from a CARA projects assignments.
- May 2009
- ShiftDiffBetweenTwoProjects.lua has been added to the script collection. It reports the combined chemical shift difference of a selected set of atomtypes in two projects (optionally using alias shifts)
- ReportAllSpectrumParameters.lua has been added to the script collection. It reports all spectrum parameters for every spectrum in a project in a table written to the CARA Terminal window.
- RecalibrateSpectra.lua has been added to the script collection. It recalibrates spectral dimensions matching a specified chemical shift range and atomtype by a fixed amount. E.g. to shift the calibration of all aliphatic 13C dimensions by 2.5
- January 2009
- RemoveAliases.lua has been updated to add a user interface. No editing of the script is necessary to execute the script on your project. The script also includes a new option to allow the removal of all alias shifts from a project. This version replaces RemoveAllAliases.lua
- Pick_3D_Peaks.lua has been updated to pick negative peaks.
- WriteAssignments.lua has been updated to write out degenerate shifts properly in BMRB's NMR-STAR 2.1 format and to allow output of only a subset of the available assignments (e.g. only Backbone). It now also allows the residue numbers to be renumbered by chain Nr.
- DefineInfo.lua has been added to script collection. After executing this script once, the command "Info( ObjectClass)" in the LUA terminal prints all available functions of a given object class. (This script has now REALLY been added to the LUA script collection)
- CalcMassOfLabeledMolecule.lua has been updated. It now includes a checkbox to calculate the expected mass for mass-spectrometry and can also calculate the mass in solution for a given pH.
- HetNoe.lua has been added to script collection. It supports the analysis of {1H}15N nOes.
2007
- November 2007
- CalcMassOfLabeledMolecule.lua has been updated in the LUA scripts. It allows the calculation of the mass of a molecule. User can now specifiy the percentages of Isotope-labeling and whether the expected mass should be calculated for Mass-Spec or in solution at a given pH.
- WriteAssignments.lua has been updated to allow a subset of the available assignments to be written out (e.g. only Backbone or only Protons)
- October 2007
- WriteAssignments.lua has been updated to write out degenerate shifts correctly in BMRB NMR-STAR 2.1 format. Each atom with the same shift is written out on a separate line and given the appropriate ambiguity code.
- HetNoe.lua has been added to the LUA scripts. It supports the analysis of {1H}15N-nOes within CARA.
- March-April 2007
- 1.8.4 includes alpha version of isotope-labeling functions. See release notes for details
- A new LUA script has been added, ShowNoesInMolmol.lua that supports NOE assignment and structure refinement. The script generates a molmol script that highlights atoms in the structure which could be involved in an NOE.
- February 2007
- 1.8.3 stable release on windows, OSX, PowerPC, solaris, irix and linux. 1.8.3 has been statically compiled so that it is not dependepent on the Microsoft CRT assembly. See release notes for additional changes.
- January 2007
- 1.8.2 did not run on some Windows Installations. This problem has been solved. See the footnote 3) on the download page and the related issue in the Tracker: http://www.cara.ethz.ch/Tracker/0785
- Updated the guide to StructureCalculation. Now there is also a "untested" section on manual structure calculation.
- 1.8.2 stable release on windows and linux.
2006
- December 2006
- 1.8.1 stable release on all major platforms. Completes the transition to the new gui library. Uses Lua 5.1 and Qt4.2. Added ability to adjust intensity display with "cw" command. Can write out spectral regions (like planes) from buffers using CALUA. See Release notes at http://www.nmr.ch for details.
- A new LUA script has been added, ShiftSpinsInCatagory.lua, that supports the adjustment of spin shifts in catagories (aromatics, amines etc...) which is helpful for calibrating shifts and correcting differences resulting from incompatible referencing of spectra during the assignment phase of a project.
- November 2006
- The new LUA script CreateOriginSystemsFromProjectedSpins.lua has been corrected for several bugs. Version 3 works.
- The IssueTracker is reopened for business! Please enter the numbers displayed in the window at the bottom of an Issue to confirm the entry. Thanks!
- 1.8.1a4 alpha release, fixes some issues related to Qt4 binding and printing.
- IssueTracker temporarily closed due to unwanted entries (unrelated to CARA)
- 1.8.1a3 alpha release completes the migration of the whole CARA/Lua binding (Gui, Spec etc.) to the new Lua5.1/Qt4.2 layer.
- 1.8.1a1 and 1.8.1a2 alpha releases of CARA. a1 is a hybrid of old and new gui library where as a2 runs entirely on the new gui library. Those interested in CARA development or providing feedback can try these releases out.
- October 2006
- Reorganized CALUA page by placing scripts into separate pages.
- A bug fix release for 1.7.0 is available 1.7.1 which can be downloaded at the usual place.
- Added the LUA script IsotopeShiftAliases.lua which creates aliases to adjust for deuterium isotope shifts in spectra measured on perdeuterated protein.
- Added the LUA script ExportSpinLinksToUpls.lua which exports spinlinks to a UPL file. Each UPL is 5.0 Angstroms.
- Updated WriteAssignmentsInFormatX.lua. the successor LUA script WriteAssignments.lua can write out alias shifts from a specific spectrum. This allows users to write out separate protonlists for each NOESY spectrum used in a structure calculation.
- Rewrote the wiki pages on HeteronuclearBackboneAssignment and HeteronuclearSidechainAssignment. There is now a section on how to use the HCCONH experiments. Also a new script was added to the CALUA page which allows assignments obtained from HCCONH experiments to be transferred into the origin system.
- September 2006
- 1.7.0 stable release of CARA incorporating Qt4.
- August 2006:
- Added a wiki page with a guide on how to interface CARA with StructureCalculation.
- New releases of CARA
- 1.7.0b1 introduces the first beta release of CARA incorporating Qt4.
- 1.7.0b2 fixes a couple of bugs in 1.7.0b1
- the ruler displays in SystemScope in 1.7.0b2
- the box around selected spins still covers the part of the label text, but it is better than before.
- July 2006:
- New releases of CARA:
- 1.5.5 fixes a problem in the contour display of folded regions resulting in an error in the picked position of up to FoldLevel? x Delta (the spectral resolution of the dim). This can result in systematic errors in the position of spins particularly when they were picked in the multiply folded regions of spectra with low resolution in the corresponding spectral dimension (e.g. 13Cmethyl spins adapted to the 13Cali dimension of 3D 13Cali NSY using CARA versions < 1.5.5). There is a script available at the CALUA page to adapt the spin shifts to the correct position: CorrectShiftsForFoldErrorInCaraBelow155.lua. The contours should agree with the corrected shifts when viewed with 1.5.5.
- 1.7.0a5 is an alpha release which introduces the new Qt4 graphics engine. Users interested in CARA development are encouraged to test the alpha version and report both suggested improvements and bugs in the IssueTracker or directly to the developer.
- IssueTracker is put back on line after an upgrade and the installation of a filter. If you find any inappropriate issues or follow-ups (items not related to CARA), please report it to the Cara Definition Team. Thanks!
- June 2006: IssueTracker temporarily taken offline due to Spam-bot. It will be up as soon as we find a way to solve the problem.
- April 2006: new and updated Lua scripts added to CALUA page
- WriteShiftsInColumns.lua writes selected atoms shifts into columns, one line per residue.
- AssignmentReport.lua writes out report on completeness of assignments and unusual chemical shifts.
- March 2006: new Lua scripts have been added to the CALUA page
- Pick_2D_Peaks.lua uses local maxima in a 2D to pick spin systems at the appropriate chemical shifts (e.g. to pick spin systems in an HSQC15N)
- Pick_3D_Peaks.lua uses local maxima in a 3D and the anchor positions of spin systems already in the project to pick spin along the strip axis at the appropriate chemical shifts
- Jan-Feb 2006: new Lua scripts have been added to the CALUA page
- ExportToXplor.lua converts spinlinks into a UPL file for X-Plor
- WriteAssignmentsInFormatX.lua writes out assignments in formats for ATNOS/CANDID automated NOE-assignment and structure calculation with DYANA or CYANA and for submission to the BMRB.
- CalcMassOfLabeledMolecule.lua calculates the molecular weight of a molecule based on the sequence in a project and accepts the percentage isotope-labeling 2H,13C,15N and d2o as input.
2005
- April 1 2005: The new Template file Start1.2.cara is released (Updated June 09 2005)
- It is fully compatible with BMRB files
- Incorporates the latest chemical shift statistics
- Improves the SpectrumType definitions
- Includes internal documentation to help users
- Contains many improved and new LUA scripts
- Is available from the TemplatesPage