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analyze_small_molecule_result.md

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Analyze small molecule result

  • In output/(run date-time)/(SPACE_GROUP)/(UNIT_CELL)
    • Space group identification
      • self-explanatory in a folder name
      • (alternatively) grep " Space group Flack_x" -A 1 shelxt_input_from_xdsconv.lxt
    • Unit cell constants identification
      • self-explanatory in a folder name
      • (alternatively) grep UNIT_CELL_CONSTANTS XSCALE.LP
    • Merged COMPLETENESS of DATA identification
      • grep COMPLETENESS -A 25 XSCALE.LP
  • In output/(run date-time)/(SPACE_GROUP)/(UNIT_CELL)/shelxl_no_cif
    • Open sol1.fcf (Coot -> File -> Open MTZ, mmCIF, fcf or phs)
    • Open sol1.res (Coot -> File -> Open Coordinates)
      • (For macOS, Coot can be installed at /Applications/ccp4-7.0)
    • Resolution can be known by _reflns_d_resolution_high
      • For example, if "grep _reflns_d_resolution_high sol1.fcf" shows _reflns_d_resolution_high 0.9003
      • the minimal resolution is 0.9003 Angstrom.
      • There are other local areas whose resolutions are worse than this minimal resolution.
      • However, it is customary to report this minimum resolution both in x-ray crystallography and cryo-EM.
  • In output/(run date-time)/(SPACE_GROUP)/(UNIT_CELL)/shelxl_with_cif
    • .cif file is generated