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铁杆木虫 (著名写手)

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[交流] cif检测三个错误，如何处理，谢谢！

晶体cif检测有三个错误，请问各位虫友如何处理？谢谢！
Alert level A
PLAT220_ALERT_2_A Large Non-Solvent C    Ueq(max)/Ueq(min) ...    5.71 Ratio
PLAT222_ALERT_3_A Large Non-Solvent H    Ueq(max)/Ueq(min) ...    7.47 Ratio
Alert level B
PLAT341_ALERT_3_B Low Bond Precision on  C-C Bonds (x 1000) Ang ..       36

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xi2004

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参见shelx说明书

SIMU  s[0.04]  st[0.08]  dmax[1.7]  atomnames
Atoms closer than dmax are restrained with effective standard deviation s to have the same Uij components. If (according to the connectivity table, i.e. ignoring attached hydrogens) one or both of the two atoms involved is terminal (or not bonded at all), st is used instead as the esd. If s but not st is specified, st is set to twice s.  If no atoms are given, all non-hydrogen atoms are understood. SIMU_* with no atoms applies to all non-hydrogen atoms in all residues. SFAC element names may also be referenced, preceded by '$'.  The interatomic distance for testing against dmax is calculated from the atom coordinates without using the connectivity table (though the latter is used for deciding if an atom is terminal or makes no bonds).

Note that SIMU should in general be given a much larger esd (and hence lower weight) than DELU; whereas there is good evidence that DELU restraints should hold accurately for most covalently bonded systems, SIMU (and ISOR) are only rough approximations to reality.  s or st may be set to zero to switch off the appropriate restraints.

SIMU is intended for use for larger structures with poorer resolution and data to parameter ratios than are required for full unrestrained anisotropic refinement.  It is based on the observation that the Uij values on neighboring atoms in larger molecules tend to be both similar and (when the resolution is poor) significantly correlated with one another.  By applying a very weak restraint of this type, we allow a gradual increase and change in direction of the anisotropic displacement parameters as we go out along a side-chain, and we restrain the motion of atoms perpendicular to a planar group (which DELU cannot influence).  The use of a distance criterion directly rather than via the connectivity table enables the restraints to be applied automatically to partially overlapping disordered atoms, for which it is an excellent approach. dmax can be set so that coordination distances to metal ions etc. are excluded.  Terminal atoms tend to show the largest deviations from equal Uij's and so st should be set higher than s (or made equal to zero to switch off the restraints altogether).  SIMU restraints are NOT recommended for SMALL molecules and ions, especially if free rotation or torsion is possible (e.g. C5H5-groups, AsF6- ions).  For larger molecular fragments, the effective rotation angles are smaller, and the assumption of equal Uij for neighboring atoms is more appropriate: both translation and libration of a large fragment will result in relatively similar Uij components on adjacent atoms.  SIMU may be combined with ISOR, which applies a further soft but quite different restraint on the Uij components.  SIMU may also be used when one or both of the atoms concerned is isotropic, in which case experience indicates that a larger esd (say 0.1 Å2) is appropriate.  The default value of s may be changed by a preceding DEFS instruction (st is then set to twice s).