ScriptsToExportFileToProgram

Scripts to export file for a Program:

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• ATNOS/CANDID & DYANA or CYANA2.0
  • 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 chemical shift assignments either for submission to BMRB (NMR-STAR 2.1 format) or in a nomenclature consistent for structure calculations using ATNOS/CANDID together with DYANA or CYANA2.0 (seq and prot files).
    • UPDATED (Ver. 9) Can write out alias shifts for a specific spectrum. Can write out shifts for a subset of all assigned shifts( e.g. only Backbone).
    • UPDATED (Ver. 10) Can number the residues by Chain Nr (e.g. Sequence-explorer "Renumber from here...")
• EXCEL
  • WriteBatchTable.lua : Write out a table from a batch integration into a text file (for EXCEL).
  • NEW 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".
  • 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.
• MARS
  • NEW WriteInputForMars.lua : Writes out input file for MARS (a program for backbone assignment)
• 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,CO,CO-1,HA,HA-1 chemical shifts for import into Excel and use with PACES.
• 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
  • WriteTalosFile.lua : Writes out a TALOS file. Thanks to Andrew Severin for the original script.
    • UPDATED (Ver. 2) Script now writes out correct format and works for projects with incomplete residue assignments.
    • UPDATED (Ver. 3) Bug causing crash fixed. Now writes out in TALOS+ format. Numbering by ChainNr?.
• XEASY
  • WriteProtonList.lua : Writes out an xeasy-formatted proton list for a project (no unassigned "999.000" atoms included)
    • NOTE A more sophisticated script for this purpose is WriteAssignments.lua (see ATNOS/CANDID section above)
  • 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. Note that you can load this peaklist back into CARA from MonoScope. Because the list is numbered by residue, this makes it convenient to use the peaklist navigator in MonoScope (pl) or the shortcut goto peak gp to find the signal from a given residue.
• 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 a PeakList? in a project. The intensities are divided into four catagories and converted into distance constraints which are written to an external file. Thanks to C. Hilty for this contribution.