Frequently asked questions

  • Question: I would like to see how your program works for my favorite molecule. How can I simulate a diffraction dataset?
  • Answer: The structure factors of your crystallographic structure (if experimental diffraction data are not available in the PDB) can be easily simulated with SFALL program, which is part of the CCP4 suite (detailed documentation can be found here). First calculate structure factors with the following script:
    sfall xyzin structure.pdb hklout structure_fc.mtz << EOF
    MODE sfcalc xyzin
    RESOLUTION 2.5
    CELL [cell parameters]
    SYMMETRY [the spacegroup number or name]
    LABOUT FC=FC PHIC=PHIC
    END
    EOF
    
    RIBER/DIBER requires a dataset containing experimental errors for each of the measured amplitudes. You can simulate them e.g. using SFTOOLS program (also a part of the CCP4 suite, detailed documentation may be found here)
    sftools << EOF
    READ structure_fc.mtz
    CALC Q COL SIGFC = col FC 0.5 **
    WRITE structure_fc_sigfc.mtz
    Y
    END
    EOF
    
    Finally you must create a unique list of reflections with uniqueify script (part of the CCP4 suite, detailed documentation is available here)
    uniqueify structure_fc_sigfc.mtz structure_fc_sigfc_uni.mtz 
    
    Now you can upload the file structure_fc_sigfc_uni.mtz to the RIBER/DIBER server or test it using the standalone verion of the software.