ScriptsToModifyProjects

Scripts to modify Projects (always back-up Repository before running these scripts - there is no undo!)

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• Global modification of projects:
  • CopyAssignmentsToProject.lua : Copies systems, spins and assignments from a source project to a target project. Can be used for merging information from two projects.The spins from a system assigned to a given residue in the source project are copied into the system assigned to the same residue in the target project. Spins that are in systems with no residue assignment can be copied into the system with the same ID in the target project (when it exists and is not assigned to a residue) or into a newly created system in the target project. Selection options allow the set of copied spins to be restricted by AtomType and type of Label.
    • NOTE This script used to be called CopySpinSystemsAndAssignmentsToAnotherProject.lua
    • UPDATE Fixed some bugs in script and added option to select only spins within a specified SpinId range (allowing recently created spins to be moved between projects).
    • NOTE Use the menu item duplicate projects to backup the target project BEFORE running script. There is no UNDO!
    • NOTE Use the menu item duplicate projects to backup the target project BEFORE running script. There is no UNDO!
• Aliases:
  • CopyAliases.lua : Copies Spin Aliases from one spectrum to another.
    • UPDATE 17.Oct.05: Fixed a bug and added a flag to keep existing aliases. (t.Overwrite)
  • IsotopeShiftAliases.lua : Creates spin aliases for heavy atoms in a selected spectrum which are adjusted for the secondary isotope shift of the attatched deuterium atoms. This is useful for including spectra measured with perdeuterated and nondeuterated protein in the same project. Thanks to N. Keller for entering values into isotope shifts table.
  • RemoveAliases.lua : Removes Spin Aliases from one spectrum or from all spectra. (This updated version includes an menu interface so that editing the script is no longer necessary. It replaces RemoveAllAlliases.lua (see below).
  • RemoveAllAliases.lua : Removes all Spin Aliases from a project.
  • PeakListToAliases.lua : Creates Spin Aliases for a selected spectrum based on an external peaklist. Intended as a workaround for the "Peaks-Import Alias Shifts" in MonoScope when the error message "Cannot import: There are ambiguous shifts" appears. See header for details.
  • ShiftSpinsAndAliases.lua : Shift a subset of selected spins and their aliases by a fixed ppm value. Can also be applied to all spins. You must edit the script header to define which project, which spins, and what the size of the ppm shift is.
• Atoms:
  • NEWCorrectAtomMagnitudes.lua : Adjusts all methyl group atom magnitudes to 3 (this fixes an error in the standard template Start1.2.cara)
• Peaks:
  • ChangePeakColorCodes.lua : changes the color code of a range of peak ids.
  • CopyPeakAmpToVol.lua : Copies Peak Amplitudes to Volumes.
  • HetNoe.lua : Uses a batchlist consisting of two spectra (noe & ref) to calculate the heteronuclear nOe (ratio of peaks) and stores the result in the Peak attribute HetNoe. It also writes the results to a file in format suitable for excel. See the beginning of the script for instructions. See the beginning of the script for instructions.
• Residues:
  • LoadProtonListOntoResidues.lua : Defines expected shifts for each residue in a sequence from the proton list. User can enter the deviation from expected 1H shift (H or Q) and deviation from expected HeteroAtom shift (C or N). This is meant to support the assignment of homologous proteins or proteins where predicted assignments are available.
• ResidueTypes:
  • LoadBmrbStats.lua : Updates ResidueType Ave,Dev values from a BMRB statistics file. See header of script for details.
    • UPDATE 23.Aug.2016 - fixed problem with reading DateStamp? because BRMB modified their format for statistics webpage.
  • DeleteAssignedPeaks.lua : Deletes all Assigned Peaks from a chosen Peaklist (peaks with label "?" in one or more dimensions remain)
• Spectra:
  • RecalibrateSpectra.lua : Recalibrates all spectrum dimensions with a shift range and atom type matching the selected values by a fixed amount. E.g. To shift all alpihatic carbon dimensions by 2.5 ppm. Often used in combination with ShiftSpinsInCatagory.lua or ShiftSpinsAndAliases.lua.
    • UPDATED Aug 26 2016 version 4 introduces a checkbox option to correct all dimensions of a selected AtomType if any one of them is involved in an INEPT to the selected NeighbourAtom? (e.g. 15N-3D NOESY can be selected based on AtomType=H and NeighbourAtom=N. If checkbox is selected, then both 1H of the experiment will be corrected by the same amount. This accounts for the fact that often all dimensions of a given AtomType within a given spectrum are calibrated the same.
  • ReportAllSpectrumParameters.lua : Reports all spectrum parameters for every spectrum in a project in a table written to the CARA Terminal window.
• Systems:
  • ChangeSystemTypes.lua : Change the System Type for a selected range of Systems. Uses a nice Menu dialog.
  • CreateOriginSystemsFromProjectedSpins.lua : Creates new spin systems using the projected spins of existing spin-systems in a selected project. E.g. you picked the spins in the (H)CCONH experiment like CA-1, CB-1, CG-1 etc. in systems i and want to create the predecessor systems i-1 containing these spins with label CA, CB, CG etc. This script will create the new spin systems i-1, fill them with spins from system i but with zero offset, and link systems i-1 as predecessors to systems i. There is an option to create only new spin-systems if they are Prolines. If the origin spin system has spins with tentative labels (?CA), these will be renamed to "?" and before copying projected spins with final labels (e.g. CA-1). NOTE: Version 3 fixes a couple of bugs in the first two releases. This one works.
    • UPDATED 29.Aug.2016 - fixed an error with the loop through all spins.
  • ImportUnassignedPeaksToNewSystems.lua : Import unassigned peaks from a 3D peaklist (two H dimensions and one HeteroAtom dimension) to new Systems. This script creates a spinsystem for each unassigned peak with a spinlink between the 1H spins. Intended for use during Structure Refinement to inspect unassigned NOESY peaks from structure calculations.
  • RemoveSelectedSystems.lua : Removes selected spin systems from project.
• Spins:
  • CorrectShiftsForFoldErrorInCaraBelow155.lua : Corrects an error in the position of folded spins resulting from an error in the contour display for CARA versions < 1.5.5. After running this script, spins should have correct shifts in folded regions using CARA 1.5.5. This script should be used before exporting shifts from projects for structure calculations if the assignment were obtained using CARA versions prior to 1.5.5. See the script header for details.
  • CreateProjectedSpins.lua : Creates spins with nonzero offset (e.g CA-1 in res.2 from CA in res.1).
    • Updated June 29, 2004. Fixed a mistake & removed Project Selection if only one Project in repository.
  • CopyProjectedSpinsToOriginSystem.lua : Creates spins with zero offset from offset spins (e.g. CA in res.1 from CA-1 in res.2)
    • UPDATED ver.3: Aug.29.2016 introduced option to overwrite origin spins (e.g. CA) with shifts of projected spins (e.g. CA-1).
  • Pick_2D_Peaks.lua : Finds local maxima in an HSQC15N and creates H/N spins with unique labels obtained from SpectrumType (usually "H"/"N") with the corresponding chemical shifts (contributed by Jimm Masse 3.29.2005)
  • Pick_3D_Peaks.lua : Finds local maxima along the strip axis of a 3D at the anchor positions H/N derived from an HSQC15N (see Pick_2D_Peaks.lua above) and creates spins with the corresponding chemical shifts (contributed by Jimm Masse 3.29.2005).
    • UPDATED Fixed a bug which prevented script from using user-defined ppm ranges.
    • UPDATED Also picks negative peaks. Modified by F.Damberger
    • NOTE You must define labels in the SpectrumTypes? so that the script can match the corresponding dimensions of the 2D and 3D. See the script header for details.
  • RenameSpins.lua : Renames all spins with Old Label to a New Label. E.g. to rename the amide proton spins with label "H" generated by importing a project from a BMRB file to "HN".
  • RemoveSpins.lua : Removes all spins with a specified Label. One can also remove ALL spins by leaving the LABEL field empty.
  • ReplaceDegenerateSpinsByGroup.lua : Removes degenerate spins and replaces them by a Group (pseudoatom). E.g. After importing from BMRB, you have PHE HE1 7.05 HE2 7.05 and would like to replace these two spins by a single pseudoatom HE 7.05. Also can eliminate degenerate shifts for spins assigned to the different atoms in a single methyl group. See script header for details.
    • Updated July 8, 2010
  • ShiftSpins.lua : Shift a subset of selected spins by a fixed ppm value Can also be applied to all spins. You must edit the script header to define which project, which spins, and what the size of the ppm shift is.
  • ShiftSpinsAndAliases.lua : Shift a subset of selected spins by a fixed ppm value Can also be applied to all spins. Uses a persistent menu. Select AtomType and Catagory (e.g. all aromatics, aliphatics, amides... etc.) a : Shift a subset of selected spins and their aliases by a fixed ppm value. Can also be applied to all spins. You must edit the script header to define which project, which spins, and what the size of the ppm shift is.
  • ShiftSpinsInCatagory.lua : Shift a subset of selected spins by a fixed ppm value. Can also be applied to all spins. Uses a persistent menu. Select AtomType and Catagory (e.g. all aromatics, aliphatics, amides... etc.)
    • UPDATED Aug. 26 2016 version 5 also shifts spins with offsets (e.g. CA-1) as long as the target systems ResidueType can be determined. Also shifts spins in Systems that are not assigned to a residue as long as a SystemType? is defined and the spins label matches a AtomName? in the SystemType?.
  • SparkyAssignmentsToCara.lua : Imports the chemical shift assignments from a Sparky assignment list file into a CARA project.
• SpinLinks:
  • DeleteAllSpinLinks.lua : Deletes all Spinlinks in selected Project.
    • Updated June 24, 2004.
  • CreateLinksToSuccessor.lua : Create Spinlinks between Spins with a certain Label in a System and a Spin with another Label in the Successor System. See Header for Details.
  • ImportLinksFromPeakList.lua : Creates !Spinlinks in a Project from a NOESY Peaklist.
  • HideLinksInSpectrum.lua : Hides spinlinks in a selected spectrum. (Turns visibility off for this spectrum).
  • UplsToSpinLinks.lua : Reads UPL file due to a specific NOESY spectrum and creates Spin Links visible in that NOESY Spectrum. Spin Link Parameters are modified so that Spin Link Rating = Constraint Distance, Code = Peak Number (peak used to derive UPL). Intended to support the analysis of structure calculations with Cara.
    • Updated August 17, 2004. Includes 3D 13C-resolved [1H,1H]-NOESYs in Spectrum Selection Dialog now.
    • Updated June 17, 2015.

      Expands pseudoatoms in cases of imcompatible assignments (pseudoatom vs real atom) in UPLfile? and project.

      Converts cyana pseudoatom nomeclature (QQ and Q atoms) automatically to IUPAC (no need to manually edit UPL files)

      Allows setting of SpinLink color for created SpinLinks.

  • DeleteSpinLinksWithinSequenceFragment.lua : Script to delete all spinlinks within a defined sequence fragment. E.g. I want to delete all the spinlinks within the fragment from residue 1 to residue 50.
  • ProposeAndShow.lua : Displays contours for proposed spinlinks in the transposed positions in up to three 3D NOESY spectra (15N-resolved, 13Cali-resolved, 13Caro-resolved: Spectrum IDs are provide by user). This allows th user to check whether the proposed spinlink shows a peak in both the transposed positions: e.g. HA -(NOE)- HN(N) and HN -(NOE)- HA(CA). Thanks to A. Severin for this script.