Space group determination: Difference between revisions
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In case of a crystal with an unknown space group (SPACE_GROUP_NUMBER=0 in [[XDS.INP]]), XDS (since [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/Release_Notes.html version June 2008]) helps the user in determination of the correct space group, by suggesting possible space groups compatible with the lattice symmetry of the data, and by calculating the R<sub>meas</sub> for these space groups. | In case of a crystal with an unknown space group (SPACE_GROUP_NUMBER=0 in [[XDS.INP]]), XDS (since [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/Release_Notes.html version June 2008]) helps the user in determination of the correct space group, by suggesting possible space groups compatible with the lattice symmetry of the data, and by calculating the R<sub>meas</sub> for these space groups. | ||
== Space group selected by XDS == | |||
XDS (or rather, the CORRECT step) makes an attempt to pick the correct space group automatically: it chooses that space group which has the highest symmetry and still a tolerable R<sub>meas</sub> compared to the R<sub>meas</sub> the data have in P1. | |||
In many cases the automatic choice may be the correct one, and re-running the CORRECT step is then not necessary. | |||
== Space group selected by | == Space group selected by user == | ||
Even if the space group selected by XDS is incorrect, the resulting list (in CORRECT.LP) should give the user enough information to pick the correct space group herself. She may then put suitable lines with SPACE_GROUP_NUMBER=, UNIT_CELL_CONSTANTS= into XDS.INP and re-run the CORRECT step to obtain the desired result. (The REIDX= line is no longer required; XDS figures the matrix out.) | |||
== Parameters influencing the automatic decision == | |||
The automatic choice is influenced by a number of decision constants that may be put into XDS.INP but which have defaults as indicated below: | |||
* MAX_CELL_AXIS_ERROR= 0.03 ! relative deviation of unconstrained cell axes from those constrained by lattice symmetry | * MAX_CELL_AXIS_ERROR= 0.03 ! relative deviation of unconstrained cell axes from those constrained by lattice symmetry | ||
* MAX_CELL_ANGLE_ERROR= 0.3 ! degrees deviation of unconstrained cell angles from those constrained by lattice symmetry | * MAX_CELL_ANGLE_ERROR= 0.3 ! degrees deviation of unconstrained cell angles from those constrained by lattice symmetry | ||
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== Notes == | == Notes == | ||
There is still the page [[Old way of Space group determination]] | There is still the old Wiki page [[Old way of Space group determination]] | ||
Revision as of 10:06, 30 June 2008
In case of a crystal with an unknown space group (SPACE_GROUP_NUMBER=0 in XDS.INP), XDS (since version June 2008) helps the user in determination of the correct space group, by suggesting possible space groups compatible with the lattice symmetry of the data, and by calculating the Rmeas for these space groups.
Space group selected by XDS
XDS (or rather, the CORRECT step) makes an attempt to pick the correct space group automatically: it chooses that space group which has the highest symmetry and still a tolerable Rmeas compared to the Rmeas the data have in P1.
In many cases the automatic choice may be the correct one, and re-running the CORRECT step is then not necessary.
Space group selected by user
Even if the space group selected by XDS is incorrect, the resulting list (in CORRECT.LP) should give the user enough information to pick the correct space group herself. She may then put suitable lines with SPACE_GROUP_NUMBER=, UNIT_CELL_CONSTANTS= into XDS.INP and re-run the CORRECT step to obtain the desired result. (The REIDX= line is no longer required; XDS figures the matrix out.)
Parameters influencing the automatic decision
The automatic choice is influenced by a number of decision constants that may be put into XDS.INP but which have defaults as indicated below:
- MAX_CELL_AXIS_ERROR= 0.03 ! relative deviation of unconstrained cell axes from those constrained by lattice symmetry
- MAX_CELL_ANGLE_ERROR= 0.3 ! degrees deviation of unconstrained cell angles from those constrained by lattice symmetry
- TEST_RESOLUTION_RANGE= 10.0 5.0 ! resolution range for calculation of Rmeas
- MIN_RFL_Rmeas= 50 ! at least this number of reflections are required
- MAX_FAC_Rmeas= 2.0 ! factor to multiply P1-Rmeas with to still be acceptable
The user may experiment with adjusting these values to make the automatic mode of space group determination more successful. However, it is much easier to just input the space group and cell parameters that the user thinks are correct.
Notes
There is still the old Wiki page Old way of Space group determination