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SHELX C/D/E: Difference between revisions
→Modes of operation: update shelxe description
(→Phasing and density modification: link to pirate) |
(→Modes of operation: update shelxe description) |
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shelxe xx [reads xx.hkl and xx.ins, phases from atoms] | shelxe xx [reads xx.hkl and xx.ins, phases from atoms] | ||
shelxe xx yy [normal mode: reads xx.hkl, yy.hkl, yy.res] | shelxe xx yy [normal mode: reads xx.hkl, yy.hkl, yy.res] | ||
shelxe xx yy zz.pdb [as above plus partial structure from zz.pdb] [NEW!] | |||
shelxe xx.phi [reads xx.phi, xx.hkl, xx.ins] | shelxe xx.phi [reads xx.phi, xx.hkl, xx.ins] | ||
shelxe xx.phi yy.pdb [reads xx.phi, xx.hkl, xx.ins, partial structure yy.pdb] [NEW!] | |||
shelxe xx.fcf [reads only xx.fcf] | shelxe xx.fcf [reads only xx.fcf] | ||
shelxe xx.phi yy [reads xx.phi, xx.hkl, xx.ins, yy.hkl] | shelxe xx.phi yy [reads xx.phi, xx.hkl, xx.ins, yy.hkl] | ||
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xx.hkl contains native data, yy.hkl contains F<sub>A</sub> and α and should have been created using SHELXC or XPREP. xx.phi has .phs format (h,k,l,F,fom,φ in free format) and can be made by renaming a .phs output file from SHELXE, but only the starting phases are read from it; if a .phi file is read, the cell and symmetry are read from xx.ins and the native F-values are read from xx.hkl. xx.fcf (from a SHELXL structure refinement) provides cell, symmetry and starting phases. The output phases are written to xx.phs, the log file is written to xx.lst and, if -b is set, improved substructure phases are output to xx.pha and revised heavy atoms to xx.hat.<br> | xx.hkl contains native data, yy.hkl contains F<sub>A</sub> and α and should have been created using SHELXC or XPREP. xx.phi has .phs format (h,k,l,F,fom,φ in free format) and can be made by renaming a .phs output file from SHELXE, but only the starting phases are read from it; if a .phi file is read, the cell and symmetry are read from xx.ins and the native F-values are read from xx.hkl. xx.fcf (from a SHELXL structure refinement) provides cell, symmetry and starting phases. The output phases are written to xx.phs, the log file is written to xx.lst and, if -b is set, improved substructure phases are output to xx.pha and revised heavy atoms to xx.hat.<br> | ||
The first | The first six modes provide density modification starting from atoms and/or phases, the seventh is an inverse cross-Fourier for finding heavy atoms for a second derivative (yy) with the same origin as the first (xx), and the last mode is useful to confirm the heavy atom substructure from the final refined phases. This is useful as a post-mortem if SAD or MAD phasing fails but the structure could be solved by other means. For these last two modes, the phases for the inverse Fourier are (φ<sub>nat</sub> – α), where φ<sub>nat</sub> may be refined (-m etc.) and α is taken from yy.hkl. A few cycles of phase refinement may reduce the noise in such maps by improving the weights.<br> | ||
=== Phasing and density modification === | === Phasing and density modification === | ||