OMIT s [-3] 2-theta(lim) s is a threshold for flagging reflections as 'unobserved'. Note that if no OMIT instruction is given, ALL reflections except those with large negative Fo2 [i.e. Fo2 < -3*sigma(Fo2)] are treated as 'observed'. Unobserved data are not used for least-squares refinement or Fourier calculations, but are retained for the calculation of R-indices based on all data, and may also appear (flagged with an asterisk) in the list of reflections for which Fo2 and Fc2 disagree significantly. Internally in the program s is halved and applied to Fo2, so for positive Fo2 the test is roughly equivalent to suppressing all reflections with Fo < s*sigma(Fo), as required for consistency with SHELX-76. Note that s may be set to 0 (to suppress reflections with negative Fo2) or (as in the default setting) to a negative threshold (to suppress very negative Fo2) which has no equivalent in SHELX-76. An OMIT instruction with a positive s value is NOT ALLOWED in combination with ACTA, because it may introduce a bias in the final refined parameters; individual aberrant reflections may still be suppressed using OMIT h k l, even when ACTA is used.
2-theta(lim) defines a limiting 2-theta above which reflections are totally ignored; they are rejected immediately on reading in. This facility may be used to save computer time in the early stages of structure refinement, and is also sometimes useful for macromolecules, but should not be used without very good reason! The SHEL command may be used to flag reflections as 'unobserved' (but retain them in the data set) above or below particular 2-theta limits.
OMIT h k lThe reflection h k l is flagged as 'unobserved' in the list of merged reflections after data reduction. Since there may be perfectly justified reasons for ignoring individual reflections (e.g. when a reflection is truncated by the beam stop) this form of OMIT is allowed with ACTA; however it should not be used indiscriminately. OMIT takes effect after MERG, so if the default MERG 2 is used, OMIT must refer to the indices in the final reflection list, not necessarily as input. It will always be safe to use the indices as given in the list of reflections which do not agree well that is printed after least-squares refinement; however if no sort-merge is performed, OMIT suppresses all reflections with matching indices.
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OMIT atomnamesThe named atoms are retained in the atom list but ignored in the structure factor calculation and least-squares refinement. This instruction may be used, together with L.S. 0 and FMAP 2, to create an 'OMIT map' to get a clearer picture of disordered regions of the structure; this concept will be familiar to macromolecular crystallographers. In particular, 'OMIT $H' can be used to check the hydrogen atom assignment of -OH groups etc. If an actual peak is present within 0.31 A of the calculated hydrogen atom position, the electron density appears in the 'Peak' column of the PLAN output. OMIT_* $H must be used for this if residues are employed.
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