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Old way of Space group determination: Difference between revisions
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Old way of Space group determination (view source)
Revision as of 12:36, 16 November 2007
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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 | * 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). | ||
* 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> | ||
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* repeat for each possible lattice character and finally decide on space group(s) | * repeat for each possible lattice character and finally decide on space group(s) | ||
Example | Example: | ||
LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) REINDEXING CARD (CORRECT) | LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) REINDEXING CARD (CORRECT) | ||
CHARACTER LATTICE OF FIT a b c alpha beta gamma | CHARACTER LATTICE OF FIT a b c alpha beta gamma | ||
| Line 58: | Line 58: | ||
43 mI 999.0 219.4 537.2 164.1 107.7 138.4 66.0 -1 1 0 0 -1 1 -2 0 0 -1 0 0 | 43 mI 999.0 219.4 537.2 164.1 107.7 138.4 66.0 -1 1 0 0 -1 1 -2 0 0 -1 0 0 | ||
44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 | 44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 | ||
This list is | This list is easier to digest by running [[jiffies|sortlattices]] - the top 12 sorted by "Quality of Fit (QoF)" are: | ||
44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 | 44 aP 0.0 145.8 164.1 245.4 90.1 90.0 90.1 -1 0 0 0 0 1 0 0 0 0 -1 0 | ||
31 aP 0.3 145.8 164.1 245.4 89.9 90.0 89.9 1 0 0 0 0 1 0 0 0 0 1 0 | 31 aP 0.3 145.8 164.1 245.4 89.9 90.0 89.9 1 0 0 0 0 1 0 0 0 0 1 0 | ||
| Line 72: | Line 72: | ||
37 mC 250.3 511.9 145.8 164.1 90.1 90.1 73.5 -1 0 -2 0 -1 0 0 0 0 1 0 0 | 37 mC 250.3 511.9 145.8 164.1 90.1 90.1 73.5 -1 0 -2 0 -1 0 0 0 0 1 0 0 | ||
Obviously there's a sharp increase from Lattice character 32 (QoF=2.8) to 14 (QoF=135.2) indicating that the highest symmetry spacegroups consistent with the observed pattern of Bragg reflections are oP (orthorhombic primitive). | Obviously there's a sharp increase from Lattice character 32 (QoF=2.8) to 14 (QoF=135.2) indicating that the highest symmetry spacegroups consistent with the observed pattern of Bragg reflections are oP (orthorhombic primitive). | ||
One would thus look up, in the list at the bottom, the different space groups for oP (of which P212121 is most likely), and then re-run CORRECT with | |||
SPACE_GROUP_NUMBER= 19 | |||
UNIT_CELL_PARAMETERS= 145.8 164.1 245.4 90 90 90 ! note that all angles must be exactly 90° | |||
REIDX= -1 0 0 0 0 1 0 0 0 0 -1 0 | |||
If the R-factors are good, one should then inspect the table '''REFLECTIONS OF TYPE H,0,0 0,K,0 0,0,L OR EXPECTED TO BE ABSENT (*)''' in [[CORRECT.LP]] to find out if the expected screw axes are indeed there. | |||
BRAVAIS- POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS | BRAVAIS- POSSIBLE SPACE-GROUPS FOR PROTEIN CRYSTALS | ||