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Pointless: Difference between revisions
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will make an R-factor search for the correct origin. | will make an R-factor search for the correct origin. | ||
Why "SETTING SYMMETRY-BASED"? The space group number that pointless writes into the logfile (e.g. "17") is the generic one (as in the International Tables vol A), not the specific one (which could be 17, 1017 or 2017) that is used as a special convention within CCP4 to encode which of a,b and c is the two-fold screw axis. At the same time, pointless re-indexes orthorhombic such that a<b<c : this is what is called "cell-based setting" in the pointless documentation, and unfortunately it's the default. However, users of [[XDS]], [[XSCALE]] and [[XDSCONV]] want the "symmetry-based setting" because these programs do not understand 1017 and 2017 (and those numbers are not even in the logfile, only in the MTZ file). This also affects space group 18 ("P 21 21 2"), and in space group 5 the distinction between space groups C2 and I2. | Why "SETTING SYMMETRY-BASED"? The space group number that pointless writes into the logfile (e.g. "17") is the generic one (as in the International Tables vol A), not the specific one (which could be 17, 1017 or 2017) that is used as a special convention within CCP4 to encode which of a,b and c is the two-fold screw axis. At the same time, pointless re-indexes orthorhombic such that a<b<c : this is what is called "cell-based setting" in the pointless documentation, and unfortunately it's the pointless default. However, users of [[XDS]], [[XSCALE]] and [[XDSCONV]] want the "symmetry-based setting" because these programs do not understand 1017 and 2017 (and those numbers are not even in the logfile, only in the MTZ file). This also affects space group 18 ("P 21 21 2"), and in space group 5 the distinction between space groups C2 and I2. | ||
This is discussed under the headings "A note on setting conventions" and "SETTING CELL_BASED || SYMMETRY-BASED || C2" in the [http://www.ccp4.ac.uk/html/pointless.html pointless documentation]. | This is discussed under the headings "A note on setting conventions" and "SETTING CELL_BASED || SYMMETRY-BASED || C2" in the [http://www.ccp4.ac.uk/html/pointless.html pointless documentation]. | ||
What can go wrong when using the default? For example, the space group assignment of data sets differing a tiny amount in two cell parameters may flip between two alternatives, i.e. the assignment is not stable. E.g. two datasets from a P222<sub>1</sub> crystal with axes of 100,120.5,120.7 and 100,120.7,120.5 would be considered (and re-indexed!) by cell-based assignment as P222<sub>1</sub> and P22<sub>1</sub>2, respectively, with ugly consequences for data merging and all downstream steps of data usage. The example shows that enforcing a<b<c would be considered more important than assigning the spacegroup in a reliable way, which makes little sense. | |||
The upshot is: for space groups 5, 17 and 18, XDS users want to use the "symmetry-based setting", and it does not hurt to ''always'' use it, i.e. for all 65 space groups that proteins crystallize in. This deviation from the default of pointless has several advantages (avoiding the ambiguity, and avoiding change of space group assignment upon small change of axes), and no disadvantage. | The upshot is: for space groups 5, 17 and 18, XDS users want to use the "symmetry-based setting", and it does not hurt to ''always'' use it, i.e. for all 65 space groups that proteins crystallize in. This deviation from the default of pointless has several advantages (avoiding the ambiguity, and avoiding change of space group assignment upon small change of axes), and no disadvantage. | ||