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User Scripts:
These Scripts have been provided by CARA users for other CARA users "as is" with no guarantees. Always back-up your repository before running a script.
. Some of them may require some editing of the script to apply them to your project. After Importing the LUA script, Open it and read the header.
The scripts are organized into catagories according to what they do:
Catagories of scripts
- ResidueTypes:
- CorrectAtomMagnitudes.lua : Adjusts all methyl group atom magnitudes to 3 (this fixes an error in the standard template Start1.2.cara)
- LoadBmrbStats.lua : Updates ResidueType Ave,Dev values from a BMRB statistics file. See header of script for details.
- UPDATE Aug.29 2016: BMRB changed their datestamp format from MO-DAY-YEAR to MO/DAY/YEAR, updated script to read this. Also added check for IUPAC nomenclature and script now stores the value of SDmult as Attribute of each modified ResidueType. See header for details.
- AssignmentReport.lua : Writes out a report of chemical shift assignments to either terminal window or to a file. Identifies unusual shifts. It is possible to filter for only missing assignments (H atoms only or also heteroatoms).
- CalcMassOfLabeledMolecule.lua : Calculates the molecular weight of a sequence in a project assuming the isotope-enrichment and percent d2o entered by the user. 2H, 13C, and 15N are available by default. Other nuclei can be accessed by commenting in an option at the top of the script.
- UPDATED includes a checkbox to calculate the expected mass for mass-spectrometry and can also calculate the mass in solution for a given pH.
- ChemShiftDeviationsFile.lua : Writes a file containing Chemical Shift Deviations from the average values stored in the repository library. See also ChemShiftDeviationsPlot.lua
- ChemShiftMapFromTwoPeakLists.lua : Writes combined chemical shift changes to script terminal window using two peaklists as input. The two peaklists should have the same peak Ids for same peaks and ideally peaks should be numbered by residue (You can use PeakListNumberedByResidue.lua to generate them). Combined chemical shift differences are calculated using the difference in chemical shift of the peaks with same Id in the two peaklists. Script also outputs atom selections in MOLMOL format for those residues having shifts larger that StdevThreshold x standard deviation of the dataset as well as a MOLMOL selection corresponding to all peaks with color = PeakColor in PeakList1.
- CompareProjects.lua : Compares the assigned resonances and shift values in two projects - reports assignments unique to one project and shift values that differ signficantly. See also CopyAssignmentsToProject.lua
- ExportAllSpins.lua : Writes a file containing an atom list in XEASY format. All spins in the selected project are included (also CA-1 etc)
- GetLineWidthsFromPeakLists.lua : Writes out a file with one line for each peak in a peaklist reporting peaknumber and linewidth at half height along a one dimension of a 2D spectrum (see header for details)
- 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.
- UPDATE (ver.2): Improved User interface, output format and introduced the option to write out the spectrum-dependent parameter (e.g. MixTime, ExchTime)
- UPDATE 3.Jan.18 (ver.3): Added features to user interface, different options to identify overlapped peaks, color them, filter them from output file
- ReportSpinsWithColorNinPeakList.lua : Writes out a text file containing spins which occur more than N times in a peak with color C in peaklist P. (User enters N,C & P).
- ShiftDiffBetweenTwoProjects.lua : Writes out a report of the combined chemical shift differences between two projects from each residue. Optionally the alias shifts of two spectra can be used. This can be useful for chemical shift mapping.
- SideChainDeviations.lua : Writes out a report of average deviation of chemical shifts from each residue normalized to the standard deviation of the database versus residue number (H atoms only or also heteroatoms).
- WriteShiftsInColumns.lua : Writes out shifts for selected atoms into columns, one line per residue. The user can edit a table at the beginning of the script to define which atoms shifts are written out. Currently: "H", "HA", "CA", "CB".
- Analysis Reports to Script Window or to File:
- AssignmentReport.lua : Writes out a report of chemical shift assignments to either terminal window or to a file. Identifies unusual shifts. It is possible to filter for only missing assignments (H atoms only or also heteroatoms).
- CalcMassOfLabeledMolecule.lua : Calculates the molecular weight of a sequence in a project assuming the isotope-enrichment and percent d2o entered by the user. 2H, 13C, and 15N are available by default. Other nuclei can be accessed by commenting in an option at the top of the script.
- ChemShiftDeviationsFile.lua : Writes a file containing Chemical Shift Deviations from the average values stored in the repository library. See also ChemShiftDeviationsPlot.lua
- ExportAllSpins.lua : Writes a file containing an atom list in XEASY format. All spins in the selected project are included (also CA-1 etc)
- ReportSpinsWithColorNinPeakList.lua : Writes out a text file containing spins which occur more than N times in a peak with color C in peaklist P. (User enters N,C & P).
- SideChainDeviations.lua : Writes out a report of average deviation of chemical shifts from each residue normalized to the standard deviation of the database versus residue number (H atoms only or also heteroatoms).
- WriteAssignments.lua : Writes out assignments for BMRB, DYANA, CYANA or CARA (see entry for WriteAssignments.lua script in section "Export File for a Program" below for details)
- WriteShiftsInColumns.lua : Writes out shifts for selected atoms into columns, one line per residue. The user can edit a table at the beginning of the script to define which atoms shifts are written out. Currently: "H", "HA", "CA", "CB".
- Export File for a Program:
- ATNOS/CANDID, DYANA, CYANA
- ExportSpinLinksToUpls.lua : Writes a UPL file in CYANA format containing one UPL for each spinlink connecting the atoms corresponding to the linked spins. The upper distance limits are all set to 5.0 Angstroms. This script can be used together with UplsToSpinLinks.lua in order to transfer spinlinks from one project to another. Thanks to D. Frueh for this contribution.
- WriteAssignments.lua : Writes out assignments in a nomenclature consistent for structure calculations using ATNOS/CANDID together with DYANA or CYANA (seq and prot files). Can also write out assignments for submission to BMRB, or in CARA format for transfer of assignments between projects or repositories.
- UPDATED 20.Sept.2016:
- can write out RNA/DNA assignments
- write in CARA format (see above)
- insert CYANA linker residues into sequence file for projects with multiple chains
- chemical shift errors input by user are nolonger ignored
- UPDATED 25. Apr. 2017 - fixed bug "attempt to perform arithmetic on global
NumAssignedAtoms (a nil value)"
- UPDATE 07. Oct. 2019 - fixed issue when BMRB format is written out using alias shifts (it wrote global shifts or gave the error: "[string "WriteAssignments"]:856: calling
getShift on bad self (Lua::LuaSpectrum? expected, got table)"
- UPDATE 21. July. 2021 - Updated to support writing out in BMRB NMRSTAR 3.1 format - thanks to Alvar Gossert!"
- EXCEL
- WriteBatchTable.lua : Write out a table from a batch integration into a text file (for EXCEL).
- 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.
- UPDATE (ver.2): Improved User interface, output format and introduced the option to write out the spectrum-dependent parameter (e.g. MixTime, ExchTime)
- UPDATE 3.Jan.18 (ver.3): Added features to user interface, different options to identify overlapped peaks, color them, filter them from output file
- WriteTitrationCurveDataToFile.lua : Writes chemical shift values of spins with a user-selected label for a series of spectra into a spreadsheet file. (shifts are taken from the alias values in each spectrum). See header for details.
- UPDATE 2.Jan.05: Fixed an error in line "t.Line = LineTable..." and added dialog for Project selection and entry of ProtonListName
- MARS
- MOLMOL
- ShowNoesInMolmol.lua : Writes out a molmol macro which highlights a selected target atom in cyan and all candidate atoms within a tolerance range of a user-determined chemical shift. Useful for NOE assignment during structure refinement. See header for details
- PACES
- ExportToPaces.lua : Writes out a comma-separated list of HN,N,CA,CB chemical shifts for import into Excel and use with PACES.
- UPDATE 20. May 05: Adjusted formatting to more closely adhere to PACES. Included CO, CO-1, HA, HA-1.
- SPARKY
- WriteSparkyPeakList.lua : Writes out a peaklist in sparky format from a Peaklist in a CARA project.
- UPDATED (Ver. 2) Script now writes out sparky format for 2D, 3D and 4D peaklists.
- TALOS+
- Topspin
- Write15NHSQC2DPeaksToXml.lua : Writes out a 2D 15N HSQC peaklist in Topspin XML format from a selected projects assignments. Thanks to G.Courtade.
- Write13CaliHSQC2DPeaksToXml.lua : Writes out a 2D 13Cali HSQC peaklist in Topspin XML format from a selected projects assignments. Thanks to G.Courtade for original script and A. Gossert for modification to generate 2D peaklists.
- XEASY
- WriteProtonList.lua
: Writes out an xeasy-formatted proton list for a project (no unassigned "999.000" atoms included)
- PeakListNumberedByResidue.lua : Write out a peaklist where the peaknumber corresponds to the residue number for a specific atom in each dimension. E.g. you want to write out a peaklist for an HSQC15N where each residue gives rise to a peak (HN/N) whose peaknumber corresponds to the residue number. This is useful for plotting the results of NH dynamics or exchange vs. sequence.
- X-PLOR
- ExportToXplor.lua : Converts spinlinks from a project into upper distance limits with the maximum distance (5.5A) Thanks to S. Ilin for this contribution.
- PeakListToXplorConstraints.lua : Generates a XPLOR-NIH constraints file from an integrated 2D NOESY PeakList? in a project. The intensities are divided into four categories and converted into distance constraints which are written to an external file. Thanks to C. Hilty for this contribution.
- UPDATED
* fixed an error in sorting of NOE volumes causing incorrect pairing of NOE/constraint with the assignment
- fixed errors occuring when residue assignments could not be found for peaks, or the residue/atom name of the assigned spins were not found in the IUPAC to X-PLOR conversion table.
- now sorts constraints by assignment
- summarizes number of NOE constraints in each category
- OneLetterFileToSeqFile.lua : Converts a file containing an amino acid sequence in one letter code to an XEASY seq file for easy read in to CARA. It ignores case and all characters which do not code for one of the 20 standard amino acids. Copy-paste from ExPASy? or NCBI website directly into a
.aa file and convert to .seq file!
- XeasySeqToThreeLetter.lua : Converts an xeasy
.seq file including the charges like ARG+,GLU- to a file with simple three letter code which can be read into the standard template Start1.2.cara to create a new project with sequence.
- XeasyToBmrBLabelsInProtonList.lua : Converts a protonlist using Xeasy nomenclature into one using the Bmrb nomenclature so that the converted file can used to import the shifts into a repository derived from the standard template Start1.2.cara. Use this together with "XeasySeqToThreeLetter.lua" to import Xeasy projects
- DefineInfo.lua : After executing this script once, the command "Info( ObjectClass)" in the LUA terminal prints all available functions of a given object class.
- printkeycode.lua : returns the code of the pressed key (trivial).