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Editor: damberger
Time: 2016/08/29 10:44:11 GMT+2 |
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Note: list script catagories alphabetically (except global changes which are at start) |
removed: - added: * Peaks: * <a href="ChangePeakColorCodes.lua">!ChangePeakColorCodes.lua</a> : changes the color code of a range of peak ids. * <a href="CopyPeakAmpToVol.lua">!CopyPeakAmpToVol.lua</a> : Copies Peak Amplitudes to Volumes. * <a href="DeleteAssignedPeaks.lua">!DeleteAssignedPeaks.lua</a> : Deletes all Assigned Peaks from a chosen Peaklist (peaks with label "?" in one or more dimensions remain) * <a href="HetNoe.lua">!HetNoe.lua</a> : 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. changed: - Please see script catagory Scripts to modify respository global values - - * Peaks: - - * <a href="ChangePeakColorCodes.lua">!ChangePeakColorCodes.lua</a> : changes the color code of a range of peak ids. - - * <a href="CopyPeakAmpToVol.lua">!CopyPeakAmpToVol.lua</a> : Copies Peak Amplitudes to Volumes. - - * <a href="DeleteAssignedPeaks.lua">!DeleteAssignedPeaks.lua</a> : Deletes all Assigned Peaks from a chosen Peaklist (peaks with label "?" in one or more dimensions remain) - - * <a href="HetNoe.lua">!HetNoe.lua</a> : 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. Please see script catagory Scripts to modify respository globally added: * Spins: * <a href="CorrectShiftsForFoldErrorInCaraBelow155.lua">!CorrectShiftsForFoldErrorInCaraBelow155.lua</a> : 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 versions 1.5.5 or higher. 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. * <a href="CreateProjectedSpins.lua">!CreateProjectedSpins.lua</a> : 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. * <a href="CopyProjectedSpinsToOriginalSystem.lua">!CopyProjectedSpinsToOriginalSystem.lua</a> : Creates spins with zero offset from offset spins (e.g. CA in res.1 from CA-1 in res.2) * <a href="Pick_2D_Peaks.lua">Pick_2D_Peaks.lua</a> : 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) * <a href="Pick_3D_Peaks.lua">Pick_3D_Peaks.lua</a> : 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** Now includes a menu interface to select project, 3D, threshhold, spectral region, and label for the spins. Modifed by F.Damberger * **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. * <a href="RenameSpins.lua">!RenameSpins.lua</a> : 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". * <a href="RemoveSpins.lua">!RemoveSpins.lua</a> : Removes all spins with a specified Label. One can also remove ALL spins by leaving the LABEL field empty. * <a href="ReplaceDegenerateSpinsByGroup.lua">!ReplaceDegenerateSpinsByGroup.lua</a> : 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. See script header for details. * <a href="ShiftSpins.lua">!ShiftSpins.lua</a> : 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. * <a href="ShiftSpinsInCatagory.lua">!ShiftSpinsInCatagory.lua</a> : 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. * <a href="ShiftSpinsAndAliases.lua">!ShiftSpinsAndAliases.lua</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. * <a href="SparkyAssignmentsToCara.lua">!SparkyAssignmentsToCara.lua</a> : Imports the chemical shift assignments from a Sparky assignment list file into a CARA project. * !SpinLinks: * <a href="CreateLinksToSuccessor.lua">!CreateLinksToSuccessor.lua</a> : 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. * <a href="DeleteAllSpinLinks.lua">!DeleteAllSpinLinks.lua</a> : Deletes all Spinlinks in selected Project. * Updated June 24, 2004. * <a href="ImportLinksFromPeakList.lua">!ImportLinksFromPeakList.lua</a> : Creates Spinlinks in a Project from a NOESY Peaklist. * <a href="HideLinksInSpectrum.lua">!HideLinksInSpectrum.lua</a> : Hides spinlinks in a selected spectrum. (Turns visibility off for this spectrum). * <a href="UplsToSpinLinks.lua">!UplsToSpinLinks.lua</a> : 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** 17.08.2004. 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. * <a href="DeleteSpinLinksWithinSequenceFragment.lua">!DeleteSpinLinksWithinSequenceFragment.lua</a> : 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. removed: - * Spins: - - * <a href="CorrectShiftsForFoldErrorInCaraBelow155.lua">!CorrectShiftsForFoldErrorInCaraBelow155.lua</a> : 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 versions 1.5.5 or higher. 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. - - * <a href="CreateProjectedSpins.lua">!CreateProjectedSpins.lua</a> : 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. - - * <a href="CopyProjectedSpinsToOriginalSystem.lua">!CopyProjectedSpinsToOriginalSystem.lua</a> : Creates spins with zero offset from offset spins (e.g. CA in res.1 from CA-1 in res.2) - - * <a href="Pick_2D_Peaks.lua">Pick_2D_Peaks.lua</a> : 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) - - * <a href="Pick_3D_Peaks.lua">Pick_3D_Peaks.lua</a> : 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** Now includes a menu interface to select project, 3D, threshhold, spectral region, and label for the spins. Modifed by F.Damberger - - * **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. - - * <a href="RenameSpins.lua">!RenameSpins.lua</a> : 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". - - * <a href="RemoveSpins.lua">!RemoveSpins.lua</a> : Removes all spins with a specified Label. One can also remove ALL spins by leaving the LABEL field empty. - - * <a href="ReplaceDegenerateSpinsByGroup.lua">!ReplaceDegenerateSpinsByGroup.lua</a> : 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. See script header for details. - - * <a href="ShiftSpins.lua">!ShiftSpins.lua</a> : 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. - - * <a href="ShiftSpinsInCatagory.lua">!ShiftSpinsInCatagory.lua</a> : 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. - - * <a href="ShiftSpinsAndAliases.lua">!ShiftSpinsAndAliases.lua</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. - - * <a href="SparkyAssignmentsToCara.lua">!SparkyAssignmentsToCara.lua</a> : Imports the chemical shift assignments from a Sparky assignment list file into a CARA project. - - * !SpinLinks: - - * <a href="CreateLinksToSuccessor.lua">!CreateLinksToSuccessor.lua</a> : 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. - - * <a href="DeleteAllSpinLinks.lua">!DeleteAllSpinLinks.lua</a> : Deletes all Spinlinks in selected Project. - - * Updated June 24, 2004. - - * <a href="ImportLinksFromPeakList.lua">!ImportLinksFromPeakList.lua</a> : Creates Spinlinks in a Project from a NOESY Peaklist. - - * <a href="HideLinksInSpectrum.lua">!HideLinksInSpectrum.lua</a> : Hides spinlinks in a selected spectrum. (Turns visibility off for this spectrum). - - * <a href="UplsToSpinLinks.lua">!UplsToSpinLinks.lua</a> : 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** 17.08.2004. 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. - - * <a href="DeleteSpinLinksWithinSequenceFragment.lua">!DeleteSpinLinksWithinSequenceFragment.lua</a> : 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. -
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Sys
(a nil value)".NOTE: It is now possible to overlay contours in different colors in PolyScope? (and to plot them in PrintPreview?). See Release 1.1.4. This script is kept here as a demonstration of how to use LUA to build custom scopes.
Sys
(a nil value)".UPDATE Dec. 2, 2011 ver. 3: fixed a bug which caused a crash. Now writes out TALOS+ format. Numbering by ChainNr?.
duplicate projects
to backup the target project BEFORE running script. There is no UNDO!Please see script catagory Scripts to modify respository globally
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.