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Solve a small-molecule structure: Difference between revisions
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→use XPREP to find possible spacegroups
(→Solve the structure with SHELXD: add GS posting) |
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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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=== use [[XPREP]] to find possible spacegroups === | === use [[XPREP]] to find possible spacegroups === | ||
There is no longer a need to use [[xds:XDSCONV|XDSCONV]] to convert the XDS_ASCII.HKL reflection file to HKLF 4 format (which is what the SHELX programs read) since XPREP can read XDS_ASCII.HKL directly. Just run | |||
xprep | |||
without a filename, and when the filename prompt appears, enter: | |||
XDS_ASCII.HKL | |||
(or whatever you have renamed it to) and then hit <Enter> several times until the program suggests a list of spacegroups - this list is going to be important. It may help to observe whether the data are centrosymmetric or not, from the 8th non-blank line below. Fortunately, this time there's only one spacegroup consistent with the data: | |||
<pre> | <pre> | ||
SPACE GROUP DETERMINATION | SPACE GROUP DETERMINATION | ||
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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 | ||
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HKLF 4 | HKLF 4 | ||
END | END | ||
Compared to the P1 setting that CORRECT chose, XPREP has re-indexed the data in this example such that the conventional setting is obtained for this space group. | |||
If necessary XPREP can read in several XDS_ASCII.HKL files, scale them together and merge them. However it needs to start with one file to get the space group so that it knows how to merge. | |||
=== use [[ccp4dev:Symmetry_determination_with_Pointless|POINTLESS]] to find possible spacegroups === | === use [[ccp4dev:Symmetry_determination_with_Pointless|POINTLESS]] to find possible spacegroups === | ||
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UNIT_CELL_CONSTANTS= 14.433 28.704 8.488 90.000 90.000 90.000 | UNIT_CELL_CONSTANTS= 14.433 28.704 8.488 90.000 90.000 90.000 | ||
INPUT_FILE=XDS_ASCII.HKL | INPUT_FILE=XDS_ASCII.HKL | ||
OUTPUT_FILE=56.hkl | OUTPUT_FILE=56.hkl SHELX | ||
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. | 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. | ||
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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. | 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 | |||
=== Hydrogens === | |||
For the H atoms, we just move the atoms from the bottom of the .res file to those lines where the refined atoms are, if the distances to existing (heavy) atoms are close to 1 A. For hydrogens bond to C N O (and in some cases B) we could alternatively use the HFIX instruction which sets up suitable AFIX instructions for the standard 'riding H-atom' refinement (shelXle - see below - can do this with one click). This requires lines of the form | |||
HFIX 13 XXX | |||
In this example; the first digit 1 means tert-CH (2 would mean methylen-CH2, 3 would mean methyl-CH3, 4 would mean aromatic CH), and the second digit 3 means the normal riding model. XXX stands for the (heavy) atom name. For docs and more examples see [https://www.google.com/search?btnG=1&pws=0&q=hfix+shelxl]. | |||
=== Finishing the structure === | === Finishing the structure === | ||
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The difference map also shows distinct bonding electron density on most of the bonds. | The difference map also shows distinct bonding electron density on most of the bonds. | ||
== A GUI for refining small molecule structures == | |||
A GUI called shelXle written by Christian Huebschle is now available for refining small molecule crystal structures with shelxl: http://ewald.ac.chemie.uni-goettingen.de/shelx | |||