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Old way of Space group determination: Difference between revisions
Old way of Space group determination (view source)
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Space group determination can be done within [[XDS]] by following these steps: | Space group determination can be done within [[XDS]] by following these steps: | ||
* an initial data reduction in P1, using SPACE_GROUP_NUMBER=0 (or even omitting that line) | * an initial data reduction in P1, using SPACE_GROUP_NUMBER=0 (or even omitting that line) | ||
* after CORRECT has thus run in P1, one may try other spacegroups by inspecting the table '''DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE''' in [[IDXREF.LP]] (see the example below). | * after CORRECT has thus run in P1, one may try other spacegroups by inspecting the table '''DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE''' in [[IDXREF.LP]] (see the example below). The [[jiffies|sortlattices]] jiffy is useful here. | ||
* for each possible lattice character, starting with the one corresponding to highest symmetry, do: | * for each possible lattice character, starting with the one corresponding to highest symmetry, do: | ||
** look up space groups corresponding to lattice characters from the list '''BRAVAIS-TYPE / POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS''' in [[IDXREF.LP]] (repeated at bottom of this article). | ** look up space groups corresponding to lattice characters from the list '''BRAVAIS-TYPE / POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS''' in [[IDXREF.LP]] (repeated at bottom of this article). | ||
** modify SPACE_GROUP_NUMBER=<number according to that list> | ** modify SPACE_GROUP_NUMBER=<number according to that list> | ||
** modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table> | ** modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table> | ||
** modify or insert UNIT_CELL_PARAMETERS= according to table, but make them obey space group requirements | ** modify or insert UNIT_CELL_PARAMETERS= according to table, but make them obey space group requirements (e.g. orthorhombic: all angles 90°, tetragonal and trigonal: a=b, and so on). | ||
** run XDS with JOB=CORRECT. Inspect [[CORRECT.LP]] and note R-factors, I/sigma and a and b modifiers of standard deviations | ** run XDS with JOB=CORRECT. Inspect [[CORRECT.LP]] and note R-factors, I/sigma and a and b modifiers of standard deviations | ||
** for many Bravais lattices ( | ** for many Bravais lattices, there are several possible point groups (tp and tI: 4, 422; hP: 3, 6, 312, 321, 622; hR: 3, 32; cP, cF and cI: 23 and 432) and thus several possible space groups. In these cases, only the SPACE_GROUP_NUMBER has to be changed, and the CORRECT step re-run. | ||
* repeat for each possible lattice character | * repeat for each possible lattice character | ||
* finally decide on the correct Bravais lattice and point group by comparing R-factors (in particular R_meas), and, from there, come up with possible space groups by looking at the table of systematic absences along the h,0,0 0,k,0 and 0,0,l axes of the diffraction pattern. | |||