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SHELX C/D/E: Difference between revisions
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The solvent content (-s) is by far the most critical parameter for SHELXE, and it is often worth varying it in steps of about 0.05 to maximize the difference in contrast between the two enantiomorphs and the 'pseudo-free CC' (another application for a computer farm!). Usually the optimal solvent content is higher than the calculated value at low resolution (disordered side-chains?) and lower at high resolution (ordered solvent?). Sometimes it is necessary to use many (several hundred) cycles (-m) if the starting phase information is weak but the resolution is very high. For low resolution data, the use of more than 20 refinement cycles is normally counter-productive. The current values of all parameters are output at the start of the SHELXE output, the default values of other parameters will rarely need changing. | The solvent content (-s) is by far the most critical parameter for SHELXE, and it is often worth varying it in steps of about 0.05 to maximize the difference in contrast between the two enantiomorphs and the 'pseudo-free CC' (another application for a computer farm!). Usually the optimal solvent content is higher than the calculated value at low resolution (disordered side-chains?) and lower at high resolution (ordered solvent?). Sometimes it is necessary to use many (several hundred) cycles (-m) if the starting phase information is weak but the resolution is very high. For low resolution data, the use of more than 20 refinement cycles is normally counter-productive. The current values of all parameters are output at the start of the SHELXE output, the default values of other parameters will rarely need changing. | ||
The -b switch in SHELXE causes updated heavy atom positions to be written to the file name.hat (or name_i.hat). This file can be copied or renamed to the .res file (which should be saved first!) and used to recycle the heavy atoms. | The -b switch in SHELXE causes updated heavy atom positions to be written to the file name.hat (or name_i.hat). This file can be copied or renamed to the .res file (which should be saved first!) and used to recycle the heavy atoms. The graphics program [[Coot]] should be able to deduce the space group name from the symmetry operators in this file, and so a very convenient way to obtain a map after running SHELXE is to start [[Coot]], read in 'coordinates' from the .hat or _i.hat file, and then input the phases from the .phs or _i.phs files and the phases of the heavy atom substructure from the .pha or _i.pha files. It is normally necessary to increase the sigma level of the latter map (by hitting '+' several times). This procedure even works correctly when the space group has been inverted by SHELXE! <br> | ||
Good quality MAD data, a high solvent content and/or high resolution for the native data can lead to maps of high quality that can be autotraced (e.g. with wARP) immediately. The .phs files contain h, k, l, F, fom, phi and | Good quality MAD data, a high solvent content and/or high resolution for the native data can lead to maps of high quality that can be autotraced (e.g. with wARP) immediately. The .phs files contain h, k, l, F, fom, φ and σ(F) in free format and can be read directly into [[Coot]] or converted to CCP4 .mtz format using f2mtz, e.g. for further density modification exploiting NCS using the CCP4 program [[Pirate]]. Note that if the inverted heavy atom enantiomorph is the correct one, the corresponding phases are in the *_i.phs file and SHELXE may have inverted the space group (e.g. P4<sub>1</sub> to P4<sub>3</sub>), which should be taken into account when moving to other programs!<br> | ||