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Solve a small-molecule structure: Difference between revisions
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== Determine the spacegroup == | == Determine the spacegroup == | ||
There are two ways to determine the spacegroup: | |||
# use [[XPREP]] | |||
# use CCP4 [[ccp4dev:Symmetry_determination_with_Pointless|POINTLESS]] - latest docs at [http://www.ccp4.ac.uk/html/pointless.html] | |||
These two possibilities also differ in the way how to obtain a file suitable for input to the SHELX program. | |||
If there are different spacegroup possibilities then (downstream, in structure solution and refinement) we need to try all of them in turn, until we hit one that refines really satisfactorily (R-factor below, say, 5%) and gives a structure that makes sense. | If there are different spacegroup possibilities then (downstream, in structure solution and refinement) we need to try all of them in turn, until we hit one that refines really satisfactorily (R-factor below, say, 5%) and gives a structure that makes sense. | ||
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HKLF 4 | HKLF 4 | ||
END | END | ||
=== use [[ccp4dev:Symmetry_determination_with_Pointless|POINTLESS]] to find the spacegroup === | |||
Unless the spacegroup number in XDS_ASCII.HKL already indicates this, [[ccp4dev:Symmetry_determination_with_Pointless|pointless]] needs to be told that the spacegroup may not be restricted to those 65 which occur for crystals from macromolecules: | |||
echo CHIRALITY NONCHIRAL | pointless xdsin XDS_ASCII.HKL | |||
gives | |||
<pre> | |||
Zone Number PeakHeight SD Probability ReflectionCondition | |||
Zones for Laue group P m m m | |||
1 screw axis 2(1) [a] 11 0.990 0.135 *** 0.972 h00: h=2n | |||
2 screw axis 2(1) [b] 59 1.000 0.097 *** 0.986 0k0: k=2n | |||
3 screw axis 2(1) [c] 131 0.997 0.062 *** 0.994 00l: l=2n | |||
4 glide plane b(a) 3754 0.012 0.050 0.000 0kl: k=2n | |||
5 glide plane c(a) 3754 0.013 0.050 0.000 0kl: l=2n | |||
6 glide plane n(a) 3754 0.951 0.061 *** 0.988 0kl: k+l=2n | |||
7 glide plane a(b) 1961 0.953 0.050 *** 0.990 h0l: h=2n | |||
8 glide plane c(b) 1961 0.104 0.056 0.004 h0l: l=2n | |||
9 glide plane n(b) 1961 0.100 0.056 0.004 h0l: h+l=2n | |||
10 glide plane a(c) 1074 0.960 0.058 *** 0.991 hk0: h=2n | |||
11 glide plane b(c) 1074 0.080 0.058 0.003 hk0: k=2n | |||
12 glide plane n(c) 1074 0.072 0.050 0.002 hk0: h+k=2n | |||
<!--SUMMARY_END--> | |||
Possible spacegroups: | |||
-------------------- | |||
Indistinguishable space groups are grouped together on successive lines | |||
'Reindex' is the operator to convert from the input hklin frame to the standard spacegroup frame. | |||
'SysAbsProb' is an estimate of the probability of the space group based on | |||
the observed systematic absences. | |||
'Conditions' are the reflection conditions (absences) | |||
'TotProb' is a total probability estimate (unnormalised) including the probability | |||
of the crystal being centrosymmetric from the <|E^2-1|> statistic. | |||
Chiral space groups are marked '*' and centrosymmetric ones 'O' | |||
Spacegroup TotProb SysAbsProb Reindex Conditions | |||
<P n a a> ( 56) O 0.823 0.911 h00: h=2n, 0k0: k=2n, 00l: l=2n, 0kl: k+l=2n, h0l: h=2n, hk0: h=2n (zones 1,2,3,6,7,10) | |||
--------------------------------------------------------------- | |||
Selecting space group P n a a as there is a single space group with the highest score | |||
</pre> | |||
The spacegroup that was used for CORRECT does not matter. The next step then is to generate a HKLF 4 file, using XDSCONV: | |||
SPACE_GROUP_NUMBER= 56 | |||
UNIT_CELL_CONSTANTS= 14.433 28.704 8.488 90.000 90.000 90.000 | |||
INPUT_FILE=XDS_ASCII.HKL | |||
OUTPUT_FILE=56.hkl | |||
== Solve the structure with [[SHELX C/D/E|SHELXD]] == | == Solve the structure with [[SHELX C/D/E|SHELXD]] == | ||