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Scripts to write 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). This script should be run to identify problems in the assignments before using WriteAssignments.lua to write out the assignments for structure calculation or data deposition.
- UPDATE 20.May 05: Fixed a bug which occured if NOT all residues were assigned. Error message was: "line 83: attempt to index field
Sys (a nil value)".
- UPDATE 4.6.06: Includes a nice user-interface which remembers settings. Gives average offsets from random coil values. Allows user to set minimum SD to report outlier shifts. This is the version included in the latest template Start1.2.cara.
- UPDATE 19.6.07: Fixed a bug which occured when there is only one project Error message was "No projects found in repository". Added a summary of pseudoatom conflicts (assignment of both the real atom HB2 and pseudoatom HB is reported in a warning).
- UPDATE 15.Jul. 09: includes statistics for CO resonances
- 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 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.
- ChemShiftDeviationsFile.lua : Writes a file containing Chemical Shift Deviations from the average values stored in the repository library. See also ChemShiftDeviationsPlot.lua
- NEW 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.
- ExportAllSpins.lua : Writes a file containing an atom list in XEASY format. All spins in the selected project are included (also CA-1 etc)
- NEW 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.
- ReportAllSpectrumParameters.lua : Reports all spectrum parameters for every spectrum in a project in a table written to the CARA Terminal window.
- 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).
- NEW 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". This version reports an error if spins are assigned which do not occur in the ResidueType of an assigned Residue. E.g. if you assign a "CB" to a GLY, the script will stop and report an error.