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== Space group determination with ''pointless'' == | == Space group determination with ''pointless'' == | ||
The latest and currently easiest way of space group determination from a [[XDS]] formatted reflection file is via the [[pointless]] program: | The latest and currently easiest way of space group determination from a [[XDS]] formatted reflection file is ''via'' the [[pointless]] program: | ||
pointless xdsin XDS_ASCII.HKL | echo SETTING SYMMETRY-BASED | pointless xdsin XDS_ASCII.HKL | ||
From the latter pointless output, the correct space group should be deduced and CORRECT run with appropriate SPACE_GROUP_NUMBER | From the latter pointless output, the correct space group should be deduced and CORRECT run with appropriate SPACE_GROUP_NUMBER and UNIT_CELL_PARAMETERS. | ||
== Space group determination within XDS == | == Space group determination within XDS == | ||
Space group determination can be done within [[XDS]] by following these steps: | the steps below are not needed anymore since version July-2008 so don't read on! | ||
* 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). The [[jiffies|sortlattices]] jiffy is useful here. | ''Space group determination can be done within [[XDS]] by following these steps:'' | ||
* for each possible lattice character, starting with the one corresponding to highest symmetry, do: | * ''an initial data reduction in P1, using SPACE_GROUP_NUMBER=0 (or even omitting that line)'' | ||
** 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). | * ''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.'' | ||
** modify SPACE_GROUP_NUMBER=<number according to that list> | *'' for each possible lattice character, starting with the one corresponding to highest symmetry, do:'' | ||
** modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table> | ** ''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 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). | ** ''modify SPACE_GROUP_NUMBER=<number according to that list>'' | ||
** run XDS with JOB=CORRECT. Inspect [[CORRECT.LP]] and note R-factors, I/sigma and a and b modifiers of standard deviations | ** ''modify or insert REIDX=<12 numbers corresponding to the lattice character, from the table>'' | ||
** for many Bravais types (defined at [http://www.iucr.org/iucr-top/cif/cifdic_html/2/cif_sym.dic/Ispace_group.Bravais_type.html]), there are several possible point groups ( | ** ''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).'' | ||
* repeat for each possible lattice character | ** ''run XDS with JOB=CORRECT. Inspect [[CORRECT.LP]] and note R-factors, I/sigma and a and b modifiers of standard deviations'' | ||
* finally decide on the correct Bravais lattice and point group by comparing R-factors (in particular R<sub>meas</sub>), 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. | ** ''for many Bravais types (defined at [http://www.iucr.org/iucr-top/cif/cifdic_html/2/cif_sym.dic/Ispace_group.Bravais_type.html]), 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, each point group has to be tested: the SPACE_GROUP_NUMBER has to be changed to one of those consistent with the point group, and the CORRECT step re-run.'' | ||
* ''repeat for each possible lattice character'' | |||
* ''finally decide on the correct Bravais lattice and point group by comparing R-factors (in particular R<sub>meas</sub>), 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.'' | |||
Be aware of the possibility of [http://www.ccp4.ac.uk/dist/html/twinning.html twinning], and of the different, but equivalent ways to index a given diffraction pattern ([[reindexing]])! | Be aware of the possibility of [http://www.ccp4.ac.uk/dist/html/twinning.html twinning], and of the different, but equivalent ways to index a given diffraction pattern ([[reindexing]])! | ||
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== Example == | == Example == | ||
old versions of XDS produced a list sorted by Lattice Character number: | |||
LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) REINDEXING CARD (CORRECT) | LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) REINDEXING CARD (CORRECT) | ||
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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 | ||
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 |