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SHELX C/D/E: Difference between revisions
→Phasing and density modification
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would do 20 cycles density modification with a solvent content of 0.45, phasing from the first 8 heavy atoms in the yy.res file from SHELXD assuming that they are also present in the native structure (-h8), and then use the modified density to generate improved heavy atoms (-b). The switch -i may be added to invert the substructure (and if necessary the space group), this writes xx_i.phs instead of xx.phs etc., and so may be run in parallel. <br> | would do 20 cycles density modification with a solvent content of 0.45, phasing from the first 8 heavy atoms in the yy.res file from SHELXD assuming that they are also present in the native structure (-h8), and then use the modified density to generate improved heavy atoms (-b). The switch -i may be added to invert the substructure (and if necessary the space group), this writes xx_i.phs instead of xx.phs etc., and so may be run in parallel. <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> | 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 (there is a [http://cci.lbl.gov/cctbx/phase_o_phrenia.html server] to find out). 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 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 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> | ||