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SHELX C/D/E: Difference between revisions
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A big difference in the contrast between the two heavy-atom enantiomorphs usually indicates a good SHELXE solution. However in the case of SIR, both have the same contrast but one gives the inverted protein structure. The contrast is also the same for both if the heavy-atom substructure is centrosymmetric. In the case of SAD both heavy atom enantiomers then give the correct structure, for SIR the result is an uninterpretable double image. <br> | A big difference in the contrast between the two heavy-atom enantiomorphs usually indicates a good SHELXE solution. However in the case of SIR, both have the same contrast but one gives the inverted protein structure. The contrast is also the same for both if the heavy-atom substructure is centrosymmetric. In the case of SAD both heavy atom enantiomers then give the correct structure, for SIR the result is an uninterpretable double image. <br> | ||
The pseudo-free correlation coefficient (based on the comparison of | The pseudo-free correlation coefficient (based on the comparison of E<sub>o</sub> and E<sub>c</sub> for 10% of the data left out at random in the calculation of a map that is then density modified and Fourier back-transformed in the usual way) is now printed out before every Nth cycle (set by -j, the default is -j5); a value above 70% usually indicates an interpretable map. The pseudo-free CC (which is also reported in the [[hkl2map]] plot of contrast against cycle number) is also a good indication as to when the phase refinement has converged. <br> | ||
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. | ||