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Solve a small-molecule structure: Difference between revisions
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== reduce the data with your favourite data processing software == | == reduce the data with your favourite data processing software == | ||
I use [[xds:XDS]]. The decision about the spacegroup has to be postponed, but it surely helps if the correct Laue group is employed during scaling. In the case considered here, the CORRECT step suggested P222. | I use [[xds:Main_Page|XDS]]. The decision about the spacegroup has to be postponed, but it surely helps if the correct Laue group is employed during scaling. In the case considered here, the CORRECT step suggested P222. | ||
== convert the reflection file to HKLF 4 format (intensities!) == | == convert the reflection file to HKLF 4 format (intensities!) == | ||
The HKLF 4 format is what the SHELX programs read. I used [[xds:XDSCONV]] and the following XDSCONV.INP: | The HKLF 4 format is what the SHELX programs read. I used [[xds:XDSCONV|XDSCONV]] and the following XDSCONV.INP: | ||
INPUT_FILE=XDS_ASCII.HKL | INPUT_FILE=XDS_ASCII.HKL | ||
OUTPUT_FILE=temp.hkl | OUTPUT_FILE=temp.hkl | ||
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We have to go back to XPREP and try a different spacegroup. This time I use Option "2" which means "Pccn" (number 56). SHELXD (finding 25 atoms, with a "FINAL CC 88.86") and SHELXL are run in the same way as above, but this time the R1 goes down to something above 10%, which indicates that this is probably a solution. | We have to go back to XPREP and try a different spacegroup. This time I use Option "2" which means "Pccn" (number 56). SHELXD (finding 25 atoms, with a "FINAL CC 88.86") and SHELXL are run in the same way as above, but this time the R1 goes down to something above 10%, which indicates that this is probably a solution. | ||
=== general idea === | === general idea of refining a structure === | ||
Starting from a rough guess of the number of atoms, we adjust the model, guided by the refinement results. This is an iterative process, in which we repeatedly edit 56.res to reflect our change of conception of the structure, replace 56.ins with it, and run SHELXL again. | Starting from a rough guess of the number of atoms, we adjust the model, guided by the refinement results. This is an iterative process, in which we repeatedly edit 56.res to reflect our change of conception of the structure, replace 56.ins with it, and run SHELXL again. | ||
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=== assigning chemical types === | === assigning chemical types === | ||
Since we know that there's not only carbon atoms, but likely also N, O and H, we modify | Since we know that there's not only carbon atoms, but likely also N, O and H, we modify 56.ins to have | ||
SFAC C N O H | SFAC C N O H | ||
UNIT 200 100 100 40 | UNIT 200 100 100 40 | ||
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We tell SHELXL the chemical identity by putting a 1 for a C, a 2 for a N, a 3 for an O, and a 4 for a H - the number is just the order of the atom in the SFAC line. | We tell SHELXL the chemical identity by putting a 1 for a C, a 2 for a N, a 3 for an O, and a 4 for a H - the number is just the order of the atom in the SFAC line. | ||
The chemical identity of an atom can be found from geometric parameters, and electron density. The electron density can be | The chemical identity of an atom can be found from geometric parameters, and its electron density. The electron density can be displayed e.g. in [[coot]], by loading the 56.fcf file written by SHELXL. Geometric parameters (in particular distances) are listed in the 56.lst file. Typical bond distances of C-C, C=C, C-O, C=O, C-N, X-H are ..... | ||
As a proxy to electron density we can use the refined ADPs. Atoms initially called "C", but with very low U values after refinement, are most likely O or N atoms. | |||
For the H atoms, we just cut-and-paste the atoms from the bottom of the .res file into those lines where the other atoms are, if the distances to existing (heavy) atoms are close to 1 A. | |||
== Finishing the structure == | == Finishing the structure == | ||
Finally we switch to anisotropic refinement by putting an | |||
ANIS | |||
line into 56.ins . More info about refinement options is in the [[SHELXL]] article! | |||