Edit detail for WorkingWithOtherProgramsImportExport revision 7 of 7
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Editor: damberger
Time: 2016/09/18 21:14:37 GMT+2
Note: 
changed:
-   * <a href="http://www.mol.biol.ethz.ch/groups/wuthrich_group/software">XEASY</a>
   * <a href="http://triton.iqfr.csic.es/HTML-manuals/xeasy-manual/xeasy_c.html">XEASY</a>

Exporting to XEASY, MAPPER, DYANA, CYANA, ...

  • XEASY-type .prot-lists: In the CARA main window, click on the name of the project to be exported. Now select Project > Export > Atom list. If this option is grayed out and unselectable, check that you really clicked on the project name and not somewhere inside of the project.
  • XEASY-type .peaks-lists: A peak list is always associated with a spectrum. Open the corresponding spectrum in a MonoScope window (you can either select the spectrum from the Spectra list or the peaklist from the Peaklist list). In MonoScope, choose Peaks > Export Peaklist ...
  • Convert CARA-assignments to an XEASY-peaklist: Open your Spectrum in HomoScope for a 2D or PolyScope for a 3D. Use File > Export > Peaklist to generate a new XEASY peaklist from the CARA-calculated peaks (2D). For a 3D, you see the options Export > Anchor Peaklist to export only the anchors to a 2D peaklist, and Export > Strip Peaklist to export all peaks from the 3D strips to a peaklist. Note that only peaks displayed with the current settings are exported. E.g. If Show Inferred is off, inferred peaks will not be included in the peaklist. To check the results before exporting, you can instead Export to MonoScope. After inspecting the Peaks in MonoScope you can use the command Peaks > Export Peaklist to write out the peaklist.
  • MAPPER fragment lists (.fra): In the CARA main window, click on the name of the project to be exported. Now select Project > Export > Mapper File. If this option is grayed out and unselectable, check that you really clicked on the project name and not somewhere inside of the project. Note: The generated Mapper-file cannot be run immediately, since CARA has no knowledge of the MAPPER-parameters. Edit it with a text editor (in practice copy-pasting the header of any sample MAPPER .fra-file works fine.
  • DYANA/CYANA/ATNOSCANDID: Generate XEASY-output of sequence, atomlist(s) and peaklist(s). ATNOS/CANDID in the UNIO package requires sequence,atomlists and NOESY spectra. Don't forget to export the calibrations to the NOESY spectra: Select each NOESY spectrum in the CARA Explorer and right-click "write calibration". This will modify the param file. There are a number of scripts to support the export of data for structure calculation. The most important is WriteAssignments.lua which allows you to write out shifts and sequence in residue library formats appropriate for structure calculation with DYANA or CYANA. It can also write out in BMRB format for deposition of chemical shifts or to CARA format which simplifies the transfer of assignments between projects. There are also pages specifically devoted to structure calculation.
  • Other Programs: CARAs scripting languange LUA can be used to create input for other programs. (See CALUA for details)

    For currently available LUA scripts for input to other programs, go here.

Further information on these programs: