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Solve a small-molecule structure: Difference between revisions
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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. | ||
=== use [[XPREP]] to find | === use [[XPREP]] to find possible spacegroups === | ||
First, convert the reflection file to HKLF 4 format (intensities!). The HKLF 4 format is what the SHELX programs read. I used [[xds:XDSCONV|XDSCONV]] and the following XDSCONV.INP: | First, convert the reflection file to HKLF 4 format (intensities!). The HKLF 4 format is what the SHELX programs read. I used [[xds:XDSCONV|XDSCONV]] and the following XDSCONV.INP: | ||
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END | END | ||
=== use [[ccp4dev:Symmetry_determination_with_Pointless|POINTLESS]] to find | === use [[ccp4dev:Symmetry_determination_with_Pointless|POINTLESS]] to find possible spacegroups === | ||
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: | 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: | ||
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INPUT_FILE=XDS_ASCII.HKL | INPUT_FILE=XDS_ASCII.HKL | ||
OUTPUT_FILE=56.hkl | OUTPUT_FILE=56.hkl | ||
Please note that the file 56.ins has to be set up manually in this case (just take the 56.ins from above, and adjust the symops and cell parameters). The numbers after "FIND" and "PLOP" should probably be adjusted in proportion to the expected number of atoms in the asymmetric unit. | |||
== Solve the structure with [[SHELX C/D/E|SHELXD]] == | == Solve the structure with [[SHELX C/D/E|SHELXD]] == | ||
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Peaks: 99 96 89 87 86 86 82 79 79 76 76 75 75 75 73 73 72 71 69 69 67 65 63 | Peaks: 99 96 89 87 86 86 82 79 79 76 76 75 75 75 73 73 72 71 69 69 67 65 63 | ||
Fragments: 25 | Fragments: 25 | ||
This solution obviously fulfills the requirement "When the final correlation coefficient CC (after PLOP) for an atomic resolution ab initio run of SHELXD is 65% or greater, the structure is almost certainly solved." in http://shelx.uni-ac.gwdg.de/SHELX/shelxdec/shelx-de.pdf . | |||
The resulting 56.res is: | The resulting 56.res is: | ||