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SHELX C/D/E: Difference between revisions
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<p>The above command line could be used under UNIX or Windows; under UNIX the commands to run SHELXC, SHELXD and SHELXE and the instructions for SHELXC may also be combined into a single script file as shown in the following examples. In these scripts, the instructions start on the line after '<<EOF' and are terminated by 'EOF'. The instructions may be given in any order; CELL (unit-cell), SPAG (space group in PDB notation, spaces are ignored) and FIND (followed by the number of heavy atoms) must be given; the optional instructions SFAC, MIND, NTRY, SHEL, ESEL and DSUL, if present, are copied to the SHELXD input file. <br><br> | <p>The above command line could be used under UNIX or Windows; under UNIX the commands to run SHELXC, SHELXD and SHELXE and the instructions for SHELXC may also be combined into a single script file as shown in the following examples. In these scripts, the instructions start on the line after '<<EOF' and are terminated by 'EOF'. The instructions may be given in any order; CELL (unit-cell), SPAG (space group in PDB notation, spaces are ignored) and FIND (followed by the number of heavy atoms) must be given; the optional instructions SFAC, MIND, NTRY, SHEL, ESEL and DSUL, if present, are copied to the SHELXD input file. <br><br> | ||
== MAD example == | === MAD example === | ||
shelxc jia <<EOF | shelxc jia <<EOF | ||
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If the MAD experiment fails, one should insert the line 'SMAD' somewhere in the SHELXC input instructions and run the job again. This makes a MAD experiment into a SAD experiment in which a suitably weighted mean of the anomalous differences is employed and the dispersive differences are ignored. If the CC values in SHELXD come out better, this SAD approach is likely to give a better solution, but it may be then worth trying commenting out one or more of the PEAK, INFL, HREM and LREM commands to see if there is a further improvement (if just one remains, it should be renamed SAD).<br><br> | If the MAD experiment fails, one should insert the line 'SMAD' somewhere in the SHELXC input instructions and run the job again. This makes a MAD experiment into a SAD experiment in which a suitably weighted mean of the anomalous differences is employed and the dispersive differences are ignored. If the CC values in SHELXD come out better, this SAD approach is likely to give a better solution, but it may be then worth trying commenting out one or more of the PEAK, INFL, HREM and LREM commands to see if there is a further improvement (if just one remains, it should be renamed SAD).<br><br> | ||
== SAD Example == | === SAD Example === | ||
This example of thaumatin phasing by means of the native sulfur anomalous signal (Debreczeni et al., Acta Cryst. D59 (2003) 688-696) uses 1.55 Å in-house CuKalpha data: | This example of thaumatin phasing by means of the native sulfur anomalous signal (Debreczeni et al., Acta Cryst. D59 (2003) 688-696) uses 1.55 Å in-house CuKalpha data: | ||
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Here the resolution cutoff has been reduced from 2.1 Å (which SHELXC would have suggested) to 2.0 Å to improve the chances of resolving the sulfurs. The SHEL, FIND, MIND and NTRY instructions are transferred to the file thau_fa.ins for the sulfur atom location with SHELXD. Note that the phases can be improved further in this case by using more SHELXE cycles than the usual 20. <br><br> | Here the resolution cutoff has been reduced from 2.1 Å (which SHELXC would have suggested) to 2.0 Å to improve the chances of resolving the sulfurs. The SHEL, FIND, MIND and NTRY instructions are transferred to the file thau_fa.ins for the sulfur atom location with SHELXD. Note that the phases can be improved further in this case by using more SHELXE cycles than the usual 20. <br><br> | ||
== SIRAS example == | === SIRAS example === | ||
This involves the solution of the thaumatin structure using the above 1.55 Å data as native and 2.0 Å CuKalpha data from a quick iodide soak. SIRAS usually gives the best results for iodide soaks, but it is also possible in this case to use SIR (change ‘SIRA’ to ‘SIR’) or iodine SAD (change ‘SIRA’ to ‘SAD’). <br> | This involves the solution of the thaumatin structure using the above 1.55 Å data as native and 2.0 Å CuKalpha data from a quick iodide soak. SIRAS usually gives the best results for iodide soaks, but it is also possible in this case to use SIR (change ‘SIRA’ to ‘SIR’) or iodine SAD (change ‘SIRA’ to ‘SAD’). <br> | ||