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.

(http://journals.iucr.org/services/cif/checking/ABSMU_01.html)

目的：檢查線性吸收系數(shù)數(shù)值(_exptl_absorpt_coefficient_mu)與晶胞內(nèi)容的一致性。

(1) 對比原子類型符號(_atom_type_symbol)與原子吸收系數(shù)表中的元素符號并提取衍射射線類型(_diffrn_radiation_type)的AMU值。

若衍射射線類型(_diffrn_radiation_type)不是Mo、Cu或Ag，發(fā)布一般警告

? ? ? ? "Calculation of _exptl_absorpt_correction_mu not performed for this radiation type."

? ? ? ? 唯有Mo、Cu和Ag射線能夠被CHECKCIF識別并用于檢查目的；來自其他X射線管、同步加速器或中子的波長將導(dǎo)致跳過線性吸收系數(shù)(_exptl_absorpt_correction_mu)的計算。

? ? ? ? 若使用的射線為Mo、Cu或Ag但未被識別，則可能是衍射射線類型(_diffrn_radiation_type)的關(guān)鍵詞條目格式不正確。衍射射線類型(_diffrn_radiation_type)的正確格式為'Mo K\a'、'Cu K\a'或'Ag K\a'。

若RMU小于0.90或大于1.10，發(fā)布A類警告

? ? ? ? "Alert A The ratio of given/expected absorption coefficient lies outside the range 0.90 <> 1.10"

若RMU小于0.95或大于1.05，發(fā)布B類警告

? ? ? ? "Alert B The ratio of given/expected absorption coefficient lies outside the range 0.95 <> 1.05"

若RMU小于0.99或大于1.01，發(fā)布C類警告

? ? ? ? "Alert C The ratio of given/expected absorption coefficient lies outside the range 0.99 <> 1.01"

? ? ? ? 此警告并非意味著你需要應(yīng)用吸收校正或者你的吸收校正有任何的不合適。這表明CIF中線性吸收系數(shù)值(_exptl_absorpt_correction_mu)與從給定的單胞體積和單胞中每種元素類型的總數(shù)計算的值不一致。

? ? ? ? 若你的軟件使用比較早期(例如：Int. Tables, Vol. IV, 1974)或不同來源的質(zhì)量衰減系數(shù)，那么你得到的線性吸收系數(shù)值和預(yù)測值可能會有微小的差異。CHECKCIF使用的是“Int. Tables, Vol. C, 1992, Table 4.2.4.2, pp. 193-198.”中給出的元素的光子相互作用部分的數(shù)值。

? ? ? ? 若用來獲得線性吸收系數(shù)所使用的單胞體積、Z值或化學(xué)式總和(_chemical_formula_sum)與CIF中的不同，則會引起得到的數(shù)值與預(yù)測值之間的其他差異。記住化學(xué)式總和(_chemical_formula_sum)必須與存在的所有不同片段中所有元素的真實和相一致，包括任何溶劑以及所有H原子。如果由于省略少數(shù)H原子或溶劑原子而引起差異，則不對應(yīng)于模型所暗示的內(nèi)容。

? ? ? ? 若存在多個組分例如溶劑，或者其中一個組分具有無序或關(guān)于晶體學(xué)對稱元素?zé)o序，則要確保在計算Z值、化學(xué)式總和(_chemical_formula_sum)以及線性吸收系數(shù)值時各組分的比例為正確且允許的。

例：ABSMU01_ALERT_1_A The ratio of given/expected absorption coefficient lies outside the range 0.90 <> 1.10

Calculated value of mu = 0.196

Value of mu given = 0.607

解決策略：按check計算的結(jié)果修改。