ABSMU01

PROC-NAME: ABSMU01 Type_1

PURPOSE: To check that _exptl_absorpt_coefficient_mu value is consistent with the cell contents.

PROCEDURE:

SUMMATION

(1) match _atom_type_symbol with element symbol in table of atomic abs coefficients and extract the AMU value for _diffrn_radiation_type.

IF _diffrn_radiation_type is not Mo, Cu or Ag, issue a General ALERT
"Calculation of _exptl_absorpt_correction_mu not performed for this radiation type."

Only Mo, Cu and Ag radiation is recognized by CHECKCIF for these purposes; wavelengths from other X-ray tubes, synchrotrons or neutrons will cause the calculation of _exptl_absorpt_correction_mu to be skipped.
If you are using Mo, Cu or Ag radiation, but this is not recognised, the format of your keyword entry for _diffrn_radiation_type may be incorrect. The correct format for _diffrn_radiation_type is 'Mo K\a', 'Cu K\a' or 'Ag K\a'.

[Attached are AMU values by Z for CuK\a, MoK\a and AgK\a]

>>> AMU for CuK\a in barn/atom (INT TAB VOL C P193-198)

[.0655, .194, .576, 1.66, 4.15, 8.99, 17.3, 30.4, 49.8, 76.8, 114., 161., 222., 297., 388., 497., 624., 772., 940., 1130., 1350., 1590., 1850., 2130., 2460., 2800., 3140., 476., 547., 629., 719., 819., 929., 1050., 1180., 1320., 1480., 1650., 1830., 2030., 2230., 2460., 2700., 2950., 3230., 3520., 3820., 4150., 4500., 4860., 5250., 5650., 6070., 6520., 7000., 7500., 8030., 8570., 9120., 9680., 10200., 10800., 11000., 10500., 8470., 9770., 3470., 3670., 3930., 4100., 4500., 4600., 4850., 5130., 5720., 5800., 6240., 6340., 6690., 6680., 7540., 7980., 8430., 8810., 8650., 9720., 10200., 10200., 14300., 11800., 10600., 11200.]

>>> AMU for MoK\a in barn/atom (INT TAB VOL C P193-198)

[.0624, .134, .228, .383, .661, 1.15, 1.96, 3.25, 5.15, 7.86, 11.6, 16.5, 22.9, 31., 41., 53.2, 67.8, 85.1, 105., 129., 156., 186., 220., 258., 302., 349., 401., 457., 518., 586., 660., 738., 822., 911., 1000., 1100., 1210., 1320., 1430., 247., 273., 300., 332., 364., 399., 436., 476., 518., 563., 611., 662., 716., 773., 834., 898., 965., 1040., 1110., 1190., 1270., 1350., 1440., 1540., 1630., 1740., 1840., 1950., 2070., 2190., 2310., 2440., 2580., 2720., 2860., 3010., 3160., 3310., 3480., 3650., 3820., 4010., 4190., 4380., 4580., 4070., 3980., 3220., 3300., 5400., 3700., 3870., 4030.]

>>> AMU for AgK\a in barn/atom (INT TAB VOL C P193-198)

[.0614, .128, .206, .313, .479, .745, 1.17, 1.82, 2.77, 4.12, 5.96, 8.42, 11.6, 15.6, 20.6, 26.7, 34.1, 42.9, 53.2, 65.2, 78.9, 94.7, 112., 133., 155., 180., 207., 238., 271., 307., 346., 387., 433., 482., 535., 592., 652., 715., 780., 847., 922., 1150., 1070., 192., 210., 230., 251., 273., 297., 323., 350., 378., 409., 441., 475., 511., 549., 588., 630., 674., 720., 768., 819., 872., 927., 985., 1040., 1110., 1170., 1240., 1310., 1390., 1460., 1540., 1620., 1710., 1800., 1890., 1990., 2090., 2190., 2290., 2400., 2510., 2620., 2730., 2850., 2980., 3110., 3230., 3420., 3500.]

(2) SUM
TOTAMU = AMU * <number of each type in cell>

(3) CALCULATE

MU = 10 * TOTAMU / _cell_volume (ie. mu/mm)

RMU = _exptl_absorpt_coefficient_mu / MU

TEST

IF RMU is 0.90 <> 1.10 issue ALERT A
   "Alert A The ratio of given/expected absorption coefficient lies outside the range 0.90 <> 1.10"
0.95 <> 1.05 issue ALERT B
   "Alert B The ratio of given/expected absorption coefficient lies outside the range 0.95 <> 1.05"
0.99 <> 1.01 issue ALERT C
   "Alert C The ratio of given/expected absorption coefficient lies outside the range 0.99 <> 1.01"

This alert does not imply that you need to apply an absorption correction or that your absorption correction is inappropriate in any way. It indicates that your value of the linear absorption coefficient (_exptl_absorpt_correction_mu) in the CIF does not agree with the value calculated from your given unit cell volume and the total number of each element type in the unit cell.

Small differences between your value and the predicted value may arise if your software uses an older (e.g. Int. Tables, Vol. IV, 1974) or a different source of the mass attenuation coefficients. CHECKCIF uses the photon interaction cross sections for the elements given in Int. Tables, Vol. C, 1992, Table 4.2.4.2, pp. 193-198.

Other differences between your value and the predicted value will arise if the unit cell volume, Z or _chemical_formula_sum in your CIF is different from that used to obtain your value of mu. Don't forget that _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms.

If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z, _chemical_formula_sum and the linear absorption coefficient.

Full list of validation algorithms