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czqgl

铁杆木虫 (正式写手)

[交流] 散10个金币求助一个G类错误。。。急，谢谢

各位大侠：谁能帮我看看这个问题啊？
REFLT03_ALERT_4_G  WARNING: Large fraction of Friedel related reflns may
                     be needed to determine absolute structure
           From the CIF: _diffrn_reflns_theta_max           25.93
           From the CIF: _reflns_number_total               3762
           Count of symmetry unique reflns         2704
           Completeness (_total/calc)            139.13%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1058
           Fraction of Friedel pairs measured     0.391
           Are heavy atom types Z>Si present        yes
如何解决呢？我投ACTA e 上次可能因为这个原因，在提交的时候出现了B错误，PLAT915_ALERT_3_B Low Friedel Pair Coverage ...................... 21.32 Perc
高手们指点一下，如何解决，急啊。谢谢啦，有能解决者散10金币表示感谢！
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xi2004

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小木虫(金币+0.5):给个红包，谢谢回帖交流
改过的cif  已经发给你了.
不过只是把原来的alert A改没了而已.
实际上, alert G一般是无关紧要的.

你这个结构,可以试投一下acta e, 但有点悬.

首先你删了比较多的点, 而R因子还是比较高, 表明数据不是太好.

其次你的结构中没有很重的原子, 这样,用来确定绝对够型的friedel pair就需要得比较多, 而你的只有30几%, 少了.  
解决办法, 收录全球的数据.

具体参见下面的英文说明.

下面说到的相关的几点翻译如下

1. Friedel pairs 数目的确定

在.ins中加merg 3,精修后在CIF中的total reflection number
如 _reflns_number_total              2627
再把merg 3换成MERG 2,精修后在CIF中的total reflection number
如 _reflns_number_total              3762

两者相减, 得到的就是Friedel pairs 的数目.

当你利用反常散射确定绝对构型时, 在CIF中要加
  _refine_ls_abs_structure_details   'Flack (1983), XXXX Friedel pairs'

这里的XXXX 用 3762-2627 = 1035来代替.

另外,  在CIF中填加
_chemical_absolute_configuration  ad
以表明绝对构型是用反常散射确定的.

参考英文:
[An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]


2.  如何确定绝对构型

利用反常散射是很常用的一个手段.

如果你的结构中没有重于Si的元素, 又用的是Mo靶, 那么,这个方法不可靠.
如果结构中的重原子仅是  S, P or Cl,  那强烈建议用与独立点对应的所有的Friedel pair 来精修.
重原子越重, 需要的Friedel pairs的数目百分比就越少; 含中等重量的原子的结构, 建议要>50%, 这里的百分比是 friedel pairs: unique reflections.

所对应的英文是
If the structure is non-centrosymmetric with atoms HEAVIER than silicon then it is expected that Friedel pairs will be used in the refinement and that the absolute structure will be determined experimentally, even if one or more chiral centres in the molecule are already unambiguously known from the chemistry or synthesis of the compound. If the heaviest element present is S, P or Cl, then it is strongly recommended that the Friedel opposites of all symmetry-unique reflections be included in the data set. The proportion of Friedel related reflections required decreases with the increasing atomic weight of the heaviest element that is present, but for medium weight elements, it is recommended that at least 50% of the potential Friedel related reflections have been recorded. The more Friedel pairs that are present in the data set, the smaller will be the s.u. for the absolute structure parameter (Flack's x).

如果绝对构型确定了,
那么请在CIF中加以下几行

_chemical_absolute_configuration  ad
_refine_ls_abs_structure_details
'Flack (1983), 1035 Friedel pairs'
_refine_ls_abs_structure_Flack    0.092(18)

具体说明请看
http://journals.iucr.org/services/cif/checking/REFLT_03.html




TEST_3 : Type_4
For noncentrosymmetric structures, test if the _reflns_number_total count includes any Friedel-related reflections, and estimate how may and what fraction they are of the symmetry-unique count NREF. The test is divided into "heavy atom" structures (heavier atoms than Si are present) and "light atom" structures. The light-atom test includes the radiation used in order to establish if anomalous scattering is sufficient to permit the reliable determination of the absolute structure.

IF Z > Si .and. NFDRAT < 0.5 issue a General ALERT
   "WARNING: Large fraction of Friedel related reflns needed to determine absolute structure."
If the structure is non-centrosymmetric with atoms HEAVIER than silicon then it is expected that Friedel pairs will be used in the refinement and that the absolute structure will be determined experimentally, even if one or more chiral centres in the molecule are already unambiguously known from the chemistry or synthesis of the compound. If the heaviest element present is S, P or Cl, then it is strongly recommended that the Friedel opposites of all symmetry-unique reflections be included in the data set. The proportion of Friedel related reflections required decreases with the increasing atomic weight of the heaviest element that is present, but for medium weight elements, it is recommended that at least 50% of the potential Friedel related reflections have been recorded. The more Friedel pairs that are present in the data set, the smaller will be the s.u. for the absolute structure parameter (Flack's x).
If the structure is non-centrosymmetric with atoms HEAVIER than Silicon the following two line items must be present in the CIF:

  _refine_ls_abs_structure_details
  _refine_ls_abs_structure_Flack

Add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like:

  _refine_ls_abs_structure_details   'Flack (1983), XXXX Friedel pairs'

and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]



IF Z > Si .and. NFDRAT > 0.5 issue a General ALERT
   "Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF."
If the structure is non-centrosymmetric with atoms HEAVIER than silicon the following two line items must be present in the CIF:
  _refine_ls_abs_structure_details
  _refine_ls_abs_structure_Flack

We have estimated the number of Friedel related reflections in your data set from a comparison of your value of _reflns_number_total with the theoretical number calculated for the symmetry-unique portion of reciprocal space out to your stated theta(max). We ask you to check our estimate and correct as necessary. Then add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like:

  _refine_ls_abs_structure_details   'Flack (1983), XXXX Friedel pairs'

and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]

IF Z < Si .and. radiation is CuKa .and. NFDRAT < 0.5 issue a General ALERT
   "WARNING: CuKa measured Friedel data can be used to determine absolute structure in a light-atom study only if the Friedel fraction is large."
As you only have a light atom structure (heaviest element lighter than silicon), anomalous dispersion effects are very small, even with Cu radiation. The reliability of the absolute structure determination will be improved if as many Friedel pairs of reflections as possible are present in the data set. Your current data set appears to contain less than 50% of the total potential Friedel related reflections that are possible up to your stated theta(max) and the absolute structure determination is probably unreliable (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value). If you are attempting to draw any conclusions about the absolute structure from the crystallographic data, then it is strongly recommended that the Friedel opposites of all symmetry-unique reflections be included in the data set. A recollection of your data is therefore probably warranted.
If the structure is non-centrosymmetric with only atoms LIGHTER than silicon, but you believe that the crystallographic experiment has successfully determined the absolute structure, the following two line items must be present in the CIF:

  _refine_ls_abs_structure_details
  _refine_ls_abs_structure_Flack

We have estimated the number of Friedel related reflections in your data set from a comparison of your value of _reflns_number_total with the theoretical number calculated for the symmetry-unique portion of reciprocal space out to your stated theta(max). We ask you to check our estimate and correct as necessary. Then add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like:

  _refine_ls_abs_structure_details   'Flack (1983), XXXX Friedel pairs'

and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]

If no useful absolute structure parameter can be refined (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value), authors should consider merging Friedel-pair reflections before final refinement, and stating this in the _publ_section_exptl_refinement section of the CIF, along with the meaningless absolute structure parameter value (and s.u. value) obtained from any refinement with Friedel pairs, as justification of the merging of Friedel-pair data. Users of SHELXL-97 can merge Friedel-pair data with the MERG 3 instruction.



IF Z < Si .and. radiation is MoKa .and. NFDRAT > 0.05 issue a General ALERT
   "ALERT: MoKa measured Friedel data cannot be used to determine absolute structure in a light-atom study EXCEPT under VERY special conditions."
With non-centrosymmetric structures and Mo radiation, if no atoms heavier than Si are present, the DELTA-f'' terms in the scattering factor expression are very small. In such cases, if no useful absolute structure parameter can be refined (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value), authors should consider merging Friedel-pair reflections before final refinement, and stating this in the _publ_section_exptl_refinement section of the CIF, along with the meaningless absolute structure parameter value (and s.u. value) obtained from any refinement with Friedel pairs, as justification of the merging of Friedel-pair data. Users of SHELXL-97 can merge Friedel-pair data with the MERG 3 instruction.
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czqgl

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waiy2001(金币+3,VIP+0):辛苦了，呵呵，谢谢 6-10 16:52
提醒是这样的：PROC-NAME: REFLT03 Type_1/3/4

PURPOSE: To check that _reflns_number_total is close to that expected for the cell volume, symmetry and theta max.

S = SIN [_diffrn_reflns_theta_max] / _diffrn_radiation_wavelength

NREF = The number of the reflections in the SYMMETRY-UNIQUE portion of reciprocal space out to a maximum of S. All symmetry absent reflections have been removed from this count.

NREFRAT = _reflns_number_total / NREF

NREF% = NREFRAT * 100

NFRIED = MAX ( _reflns_number_total - NREF, 0)

NFDRAT = NFRIED / NREF

TEST_1 : Type_1
In the calculation of NREF the maximum and minumum h,k,l indices in the in the unque portion of reciprocal space are saved. These are compared with the _diffrn_reflns_limit_ values in the CIF. If the estimated maximum h,k,l values do not match either the CIF _max or the absolute _min values issue a General ALERT
   "ALERT: Expected hkl max differ from CIF values"
        The maximum (or minimum) limits of h, k and l given in the CIF do not correspond with those caclculated using the theta(max) value stated under _diffrn_reflns_theta_max.
Check that theta(max) has been given correctly. If so, it may be that the h,k,l index limits set during the data collection did not correspond correctly with the limits required to ensure that at least all possible unique reflections up to the specified theta(max) were collected. If one or more of the index limits was set to a too small value, truncation of the data will have occurred and the data should be recollected. This problem sometimes occurs, especially with older diffractometers, when the index limits and theta(max) must be set independently by hand and the operator forgets to check both settings.
TEST_2 : Type_3 (centrosymmetric), Type_1 (non-centrosymmetric)
Test the completeness of the reflection count in the symmetry unique portion of reciprocal space.

IF NREF%
< 85 issue ALERT A
   "Alert A: < 85% complete (theta max?)"
< 90 issue ALERT B
   "Alert B: < 90% complete (theta max?)"
< 95 issue ALERT C
   "Alert C: < 95% complete"
        The total number of symmetry-unique reflections, including all reflections considered to be "unobserved", but excluding systematically absent reflections, should be given under _reflns_number_total. If Friedel-related reflections are being treated as independent observations in order to utilise the effects of anomalous dispersion, _reflns_number_total should correspond with the total number of these independent reflections.

The expected number of unique reflections is calculated from your reported theta(max). You should first check that theta(max) has indeed been reported correctly.

It is essential that, as far as possible, at least all possible unique reflections have been recorded up to the chosen theta(max). Severe deficiencies in this regard should be rectified by recollecting the data.

If you do not know why your data are incomplete, it can sometimes be instructive to examine the reflection file by using the ASYM-VIEW option of PLATON (requires the SHELXL format .hkl or .fcf file). This will highlight the missing reflections in each layer of the data. Missing reflections that occur in strips or inner regions of the layers suggest that an incorrect data collection strategy was used or that there was some other problem with the data collection. E.g. incorrect h,k,l limits causing truncation in one or more directions, premature termination of the data collection, loss of X-rays during part of the data collection. One accidental cause of incompleteness is to choose the wrong axis to scan completely with monoclinic space groups (e.g. collecting +h, +/-k, +l reflections when b is the unique axis).

Another reason for having incomplete data can be that your (old) data reduction program is discarding reflections with negative intensity, so that only those with positive intensity are retained in the data set and reported under _reflns_number_total. In this case, you should update or replace your data reduction program so that this does not occur.

If you are using a serial diffractometer (scintillation counter), there is usually no reason that the data should not be virtually 100% complete and severe incompleteness should be investigated carefully. Low temperature devices can sometimes be a hindrance, but should not lead to a large fraction of incomplete data.

With CCD detectors, one must ensure that the data collection strategy is sufficient to cover all unique reflections. An additional scan set at a different chi or omega setting may be required to ensure that the data set is complete.

For diffractometers with only one circle (e.g. the fixed phi circle on the Stoe IPDS and Mar Research IP systems, data completeness can be more problematic. One method for mimimising incompleteness is to ensure that the crystal is mounted such that a crystal axis is NOT coincident with the phi axis (i.e. make sure your crystals are mounted in a skew orientation).

People who use CCD or IP detectors may find that just the high angle reflections are incomplete. This occurs with rectangular apertures because the corners of the detector will record to higher angles that the mid points of the sides. In such cases it will be found that the data are essentially 100% complete at a lower theta value. This information should be incorporated into the CIF by correctly filling out the following two data items which specify the theta value at which the data are essentially 100% complete and the actual completeness at this theta value:

_diffrn_reflns_theta_full
_diffrn_measured_fraction_theta_full

One means of obtaining estimates for the above two items is to use the ACTA instruction in SHELXL, together with its optional parameter. If a value is specified for 2theta on this instruction, this value will be used to correctly fill in the above two entries in the CIF. This does not truncate the data during refinement.
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czqgl

铁杆木虫 (正式写手)
Example:
We have measured to theta(max) = 28.0 deg. with 92% completeness,
but the data are virtually 100% complete to 26.3 deg.
Using ACTA 52.6 will produce the following in the CIF:

_diffrn_reflns_theta_max        28.0
_diffrn_measured_fraction_theta_max    0.920
_diffrn_reflns_theta_full        26.3
_diffrn_measured_fraction_theta_full    0.997

If the space group is centrosymmetric also test if the expected reflection count is exceeded (perhaps because symmetry absent or equivalent reflections were mistakenly counted). Type_3
IF NREF%
> 115 issue ALERT A
   "Alert A: > 15% excess reflns - sys abs data present?"
> 110 issue ALERT B
   "Alert B: > 10% excess reflns - sys abs data present?"
> 105 issue ALERT C
   "Alert C: > 5% excess reflns - sys abs data present?"
        The total number of symmetry-unique reflections, including all reflections considered to be "unobserved", but excluding systematically absent reflections, should be given under _reflns_number_total. If Friedel-related reflections are being treated as independent observations in order to utilise the effects of anomalous dispersion, _reflns_number_total should correspond with the total number of these independent reflections.

The expected number of unique reflections is calculated from your reported theta(max). You should first check that theta(max) has indeed been reported correctly.

Having excess numbers of reflections is an indication that you have not or have incorrectly merged symmetry-equivalent reflections, or that you have included the systematically absent reflections in your count of unique reflections.

Check for typographical errors and/or that you have merged the equivalent reflections correctly before refinement.

An exception to this requirement may occur if data from a non-merohedrally twinned crystal is employed, as this may result in more than one entry in the reflection file for a given set of h,k,l indices (e.g. data read into SHELXL with HKLF 5). As a result, more reflections may be used in the refinement than the apparent number of unique reflections.

A second exception might be if you deliberately choose not to merge symmetry equivalent reflections before the refinement. This procedure is not recommended and its use should be specifically mentioned under _publ_section_exptl_refinement.

TEST_3 : Type_4
For noncentrosymmetric structures, test if the _reflns_number_total count includes any Friedel-related reflections, and estimate how may and what fraction they are of the symmetry-unique count NREF. The test is divided into "heavy atom" structures (heavier atoms than Si are present) and "light atom" structures. The light-atom test includes the radiation used in order to establish if anomalous scattering is sufficient to permit the reliable determination of the absolute structure.

IF Z > Si .and. NFDRAT < 0.5 issue a General ALERT
   "WARNING: Large fraction of Friedel related reflns needed to determine absolute structure."
        If the structure is non-centrosymmetric with atoms HEAVIER than silicon then it is expected that Friedel pairs will be used in the refinement and that the absolute structure will be determined experimentally, even if one or more chiral centres in the molecule are already unambiguously known from the chemistry or synthesis of the compound. If the heaviest element present is S, P or Cl, then it is strongly recommended that the Friedel opposites of all symmetry-unique reflections be included in the data set. The proportion of Friedel related reflections required decreases with the increasing atomic weight of the heaviest element that is present, but for medium weight elements, it is recommended that at least 50% of the potential Friedel related reflections have been recorded. The more Friedel pairs that are present in the data set, the smaller will be the s.u. for the absolute structure parameter (Flack's x).

If the structure is non-centrosymmetric with atoms HEAVIER than Silicon the following two line items must be present in the CIF:

  _refine_ls_abs_structure_details
  _refine_ls_abs_structure_Flack

Add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like:

  _refine_ls_abs_structure_details   'Flack (1983), XXXX Friedel pairs'

and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]

IF Z > Si .and. NFDRAT > 0.5 issue a General ALERT
   "Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF."
        If the structure is non-centrosymmetric with atoms HEAVIER than silicon the following two line items must be present in the CIF:

  _refine_ls_abs_structure_details
  _refine_ls_abs_structure_Flack

We have estimated the number of Friedel related reflections in your data set from a comparison of your value of _reflns_number_total with the theoretical number calculated for the symmetry-unique portion of reciprocal space out to your stated theta(max). We ask you to check our estimate and correct as necessary. Then add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like:

  _refine_ls_abs_structure_details   'Flack (1983), XXXX Friedel pairs'

and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]
IF Z < Si .and. radiation is CuKa .and. NFDRAT < 0.5 issue a General ALERT
   "WARNING: CuKa measured Friedel data can be used to determine absolute structure in a light-atom study only if the Friedel fraction is large."
        As you only have a light atom structure (heaviest element lighter than silicon), anomalous dispersion effects are very small, even with Cu radiation. The reliability of the absolute structure determination will be improved if as many Friedel pairs of reflections as possible are present in the data set. Your current data set appears to contain less than 50% of the total potential Friedel related reflections that are possible up to your stated theta(max) and the absolute structure determination is probably unreliable (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value). If you are attempting to draw any conclusions about the absolute structure from the crystallographic data, then it is strongly recommended that the Friedel opposites of all symmetry-unique reflections be included in the data set. A recollection of your data is therefore probably warranted.

If the structure is non-centrosymmetric with only atoms LIGHTER than silicon, but you believe that the crystallographic experiment has successfully determined the absolute structure, the following two line items must be present in the CIF:

  _refine_ls_abs_structure_details
  _refine_ls_abs_structure_Flack

We have estimated the number of Friedel related reflections in your data set from a comparison of your value of _reflns_number_total with the theoretical number calculated for the symmetry-unique portion of reciprocal space out to your stated theta(max). We ask you to check our estimate and correct as necessary. Then add the number of Friedel pairs used in the refinement to the _refine_ls_abs_structure_details line so that it looks like:

  _refine_ls_abs_structure_details   'Flack (1983), XXXX Friedel pairs'

and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]

If no useful absolute structure parameter can be refined (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value), authors should consider merging Friedel-pair reflections before final refinement, and stating this in the _publ_section_exptl_refinement section of the CIF, along with the meaningless absolute structure parameter value (and s.u. value) obtained from any refinement with Friedel pairs, as justification of the merging of Friedel-pair data. Users of SHELXL-97 can merge Friedel-pair data with the MERG 3 instruction.

IF Z < Si .and. radiation is MoKa .and. NFDRAT > 0.05 issue a General ALERT
   "ALERT: MoKa measured Friedel data cannot be used to determine absolute structure in a light-atom study EXCEPT under VERY special conditions."
        With non-centrosymmetric structures and Mo radiation, if no atoms heavier than Si are present, the DELTA-f'' terms in the scattering factor expression are very small. In such cases, if no useful absolute structure parameter can be refined (i.e. the value of the absolute structure parameter is meaningless because of its large s.u. value), authors should consider merging Friedel-pair reflections before final refinement, and stating this in the _publ_section_exptl_refinement section of the CIF, along with the meaningless absolute structure parameter value (and s.u. value) obtained from any refinement with Friedel pairs, as justification of the merging of Friedel-pair data. Users of SHELXL-97 can merge Friedel-pair data with the MERG 3 instruction.
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czqgl(金币+10,VIP+0):谢谢您的热心帮助，感激不尽！ 6-10 18:09
把有关absolute configuration, flack parameter,
还有reflection的几行贴上来瞧瞧.
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czqgl

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_chemical_absolute_configuration     'ad'
_refine_ls_abs_structure_Flack      0.092(18)
_refine_ls_abs_structure_details
'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack      0.092(18)
_refine_ls_number_reflns               3762
_refine_ls_number_parameters           346
_refine_ls_number_restraints           0
_diffrn_reflns_theta_min          2.23
_diffrn_reflns_theta_max          25.93
_reflns_number_total             3762
_reflns_number_gt                 2885
xi2004大侠能帮助解决吗？谢谢啦。。。
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5楼2009-06-10 18:05:04
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gm3214

木虫 (正式写手)
★
小木虫(金币+0.5):给个红包，谢谢回帖交流
请问在_refine_ls_number_reflns               3762中，
3762在哪里可以找得到
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6楼2009-06-10 22:32:29
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czqgl

铁杆木虫 (正式写手)
我的是 在cif中自带的啊。。。怎么？这个数有问题吗？
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7楼2009-06-10 22:35:06
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crystalsnet

新虫 (正式写手)
非常喜欢xi2004老师的回答，能学到很多咚咚。
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9楼2009-06-11 17:48:41
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xi2004

至尊木虫 (职业作家)
引用回帖:
Originally posted by crystalsnet at 2009-6-11 17:48:
非常喜欢xi2004老师的回答，能学到很多咚咚。

客气了. 我也是现学现卖.
翻得不对的请指正.
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xi2004-emuch@163.com
10楼2009-06-11 18:06:28
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