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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]]. 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: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 [[ | The HKLF 4 format is what the SHELX programs read. I used [[xds: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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=== solving the structure with [[SHELX C/D/E|SHELXD]] === | === solving the structure with [[SHELX C/D/E|SHELXD]] === | ||
Just run "shelxd 62". You may interrupt it with Ctrl-C once it has found good solutions, as | Just run "shelxd 62". You may interrupt it with Ctrl-C once it has found good solutions, as suggested by | ||
Try 68:20 Peaks 99 96 71 68 63 55 53 51 50 48 46 45 45 44 44 43 43 43 41 40 | Try 68:20 Peaks 99 96 71 68 63 55 53 51 50 48 46 45 45 44 44 43 43 43 41 40 | ||
R = 0.417, Min.fun. = 0.853, <cos> = 0.364, Ra = 0.432 | R = 0.417, Min.fun. = 0.853, <cos> = 0.364, Ra = 0.432 | ||
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It turns out that the R-factor does not really go down properly, and this means that the spacegroup is wrong. The "FINAL CC 58.70" result from SHELXD is probably also suspiciously low, I guess. | It turns out that the R-factor does not really go down properly, and this means that the spacegroup is wrong. The "FINAL CC 58.70" result from SHELXD is probably also suspiciously low, I guess. | ||
== structure solution and refinement in the correct spacegroup == | |||
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 === | |||
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. | |||
=== assigning chemical types === | |||
Since we know that there's not only carbon atoms, but likely also N, O and H, we modify | |||
SFAC C N O H | |||
UNIT 200 100 100 40 | |||
(the actual numbers after UNIT can be taken from the .lst file of SHELXL, they don't seem to matter much.) | |||
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 display e.g. in [[coot]], by loading the .fcf file written by SHELXL. Geometric parameters (in particular distances) are listed in the .lst file. Typical bond distances of C-C, C=C, C-O, C=O, C-N, X-H are ..... | |||
Using our editor, we can cut-and-paste the atoms from the bottom of the .res file into those lines where the other atoms are. | |||
== Finishing the structure == | |||