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Solve a small-molecule structure: Difference between revisions
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→use XPREP to find possible spacegroups
Lazarenko VA (talk | contribs) |
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Maybe it should also be stated that this was a simple case, without e.g. twinning or disorder! Furthermore, the hand of the structure was not an issue. | Maybe it should also be stated that this was a simple case, without e.g. twinning or disorder! Furthermore, the hand of the structure was not an issue. | ||
== Collecting data == | |||
There's not much magic in collecting data. Problems arise from the high resolution that's required and the strength and low number of reflections. | |||
* Mount the crystal by gluing it on a steel pin. More refined approaches might exist. | |||
* High resolution is important. 0.84Å is the minimum for publication in Acta Cryst. 1.2Å is the absolute minimum for structure solution. This can generally only be achieved on a PX system with a detector on a two-theta arm. | |||
* Crystal quality is important. There should be no streaky spots, multiple lattices, etc. You can always break off small pieces if the big chunk isn't clean enough. | |||
* As there are only few spots per image, a large rotation range is usually needed for indexing. Collect ten degrees in one-degree oscillations. This is better than collecting one ten-degree oscillation because the phi angle of each reflection is more accurately determined and the background is lower. | |||
* The beam might need to be attenuated to avoid overloads. This can be done by dialing down the energy of the electron beam going into the anode. | |||
* If a heavy atom (iodine, iron, etc.) is present in the small molecule, the data can probably be phased by SAD even with Cu Kalpha. You might be able to solve it by looking at the Patterson maps. | |||
== Reduce the data with your favourite data processing software == | == Reduce the data with your favourite data processing software == | ||
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</pre> | </pre> | ||
After that, say "c" for "define unit-cell CONTENTS", and input a reasonable number of carbon atoms (I used C20). Get out of this menu with "E". Then, choose "f" for "set up shelxtl FILES". Then, answer the question "XM/SHELXD (M) or XS/SHELXS (S) format [S]:" with "m" since we're going to use shelxd for solving the structure. Answer the question about the name (I used the spacegroup number as I knew I would have to test several possibilities). Finally, "q"uit the program. This writes 56.ins : | After that, say "c" for "define unit-cell CONTENTS", and input a reasonable number of carbon atoms (I used C20). After that you will probably need to change the wavelength, because by default xprep use Mo K_alpha, you can do it by saying "R". Get out of this menu with "E". Then, choose "f" for "set up shelxtl FILES". Then, answer the question "XM/SHELXD (M) or XS/SHELXS (S) format [S]:" with "m" since we're going to use shelxd for solving the structure. Answer the question about the name (I used the spacegroup number as I knew I would have to test several possibilities). Finally, "q"uit the program. This writes 56.ins : | ||
TITL 56 in Pccn | TITL 56 in Pccn | ||
CELL 0.71073 14.4330 28.7040 8.4880 90.000 90.000 90.000 | CELL 0.71073 14.4330 28.7040 8.4880 90.000 90.000 90.000 | ||