求助啊，懂的帮我看一下有错误没有，check cif - 晶体 - 小木虫 - 学术 科研 第一站
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求助啊，懂的帮我看一下有错误没有，check cif
最近测了一个晶体结构，之前发现传了CHECK CIF生成的报告期中A类错误比较多，后来让别人给修了一次，报告里还是有A类错误，但是他说已经修好了
大家帮我看一下，这些是不是不需要修正的错误，接触这个不不久，求指教。
下面是生成的CIF报告：
Alert level A
EXPT005_ALERT_1_A _exptl_crystal_description is missing
Crystal habit description.
The following tests will not be performed.
EXPT010_ALERT_1_A _exptl_crystal_colour (_pd_char_colour for powder) is missing
Crystal colour.
The following tests will not be performed.
DIFF005_ALERT_1_A _diffrn_measurement_method is missing
Mode of intensity measurement and scan.
DIFF019_ALERT_1_A _diffrn_standards_number is missing
Number of standards used in measurement.
DIFF020_ALERT_1_A _diffrn_standards_interval_count and
_diffrn_standards_interval_time are missing. Number of measurements
between standards or time (min) between standards.
DIFF022_ALERT_1_A _diffrn_standards_decay_% is missing
Percentage decrease in standards intensity.
checkCIF publication errors
Alert level A
PUBL004_ALERT_1_A The contact author’s name and address are missing,
_publ_contact_author_name and _publ_contact_author_address.
PUBL005_ALERT_1_A _publ_contact_author_email, _publ_contact_author_fax and
_publ_contact_author_phone are all missing.
At least one of these should be present.
PUBL006_ALERT_1_A _publ_requested_journal is missing
e.g. ’Acta Crystallographica Section C’
PUBL008_ALERT_1_A _publ_section_title is missing. Title of paper.
PUBL009_ALERT_1_A _publ_author_name is missing. List of author(s) name(s).
PUBL010_ALERT_1_A _publ_author_address is missing. Author(s) address(es).
PUBL012_ALERT_1_A _publ_section_abstract is missing.
Abstract of paper in English.
你列出的项目都是与精修没啥关系的，自己添加相应的内容即可，方便的方法是找个完整的cif对照一下。 你这个报告后面都是出版格式问题，不是acta系列的杂志可以不理会。 你这些不是修 问题，就是在你的cif文件里把先关的内容天上就可以啦EXPT005_ALERT_1_A _exptl_crystal_description is missing
这个填block，EXPT010_ALERT_1_A _exptl_crystal_colour (_pd_char_colour for powder) is missing
这个就是你的晶体是什么颜色，其他的你可以再对应一下填填 你用的这个check是很严格的包括出版格式的那种吧，试试这个http://checkcif.iucr.org/
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E-mail： & QQ：8835100cif有C级错误，求高手帮助解析 - 晶体 - 小木虫 - 学术 科研 第一站
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cif有C级错误，求高手帮助解析
Format: alert-number_ALERT_alert-type_alert-level text
020_ALERT_3_C Large R(int) .................................& && & 0.10
062_ALERT_4_C Rescale T(min) & T(max) by ...................& && & 0.87
125_ALERT_4_C No _symmetry_space_group_name_Hall Given .....& && && & ?
420_ALERT_2_C D-H Without Acceptor& && & N4& &&&-& &H4A& && && && && &?
420_ALERT_2_C D-H Without Acceptor& && & N10& & -& &H10D& && && && &&&?
420_ALERT_2_C D-H Without Acceptor& && & N14& & -& &H14C& && && && &&&?
720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ......& && && & 2
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && & 1
& && && && &&&C9 H24 N2
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && & 2
& && && && &&&C9 H24 N2
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && & 3
& && && && &&&C9 H24 N2
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && & 8
& && && && &&&C H4 N2 S
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &10
& && && && &&&C H4 N2 S
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &11
& && && && &&&C H4 N2 S
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &12
& && && && &&&H2 O
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &15
& && && && &&&Br
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &16
& && && && &&&Br
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &18
& && && && &&&Br
#===============================================================================
我把理论加H去掉指认Q峰加H都不行，还是有D-H Without Acceptor，我把晶胞推了，还是有Centre of Gravity not Within Unit Cell，老板要求解决，请求高手帮助解析，谢谢！res，hkl见附件。
已经解决了没有质子受体的问题，还差Centre of Gravity not Within Unit Cell的问题，谢谢啊 120_ALERT_1_C Reported SPGR ?& && & Inconsistent with Explicit& && &P21/N
125_ALERT_4_C No _symmetry_space_group_name_Hall Given .....& && && & ?
242_ALERT_2_C Check Low& & U(eq) as Compared to Neighbors ..& && && & N17
720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ......& && && & 2
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && & 2
& && && && &&&C9 H24 N2
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && & 8
& && && && &&&C H4 N2 S
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &12
& && && && &&&H2 O
790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.#& && && &18 把不是晶胞里面的那些分子用对称性操作移到晶胞内。首先先找到对称性代码，然后对称性找出来，删掉原来的那部分原始分子，重新命名长出来的分子，搞定！ 分子太多，移了以后又有没有质子受体的问题，现在这两个问题都出现了，哎~ 谁能帮我处理一下我，我忘放hkl文件了，能处理的我直接传给您 解决了好多问题，但是现在还有问题
062_ALERT_4_C Rescale T(min) & T(max) by ...................& && & 0.87
242_ALERT_2_C Check Low& & U(eq) as Compared to Neighbors ..& && && & N17
420_ALERT_2_C D-H Without Acceptor& && & N4& &&&-& &H4A& && && && && &?
420_ALERT_2_C D-H Without Acceptor& && & N10& & -& &H10D& && && && &&&?
720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ......& && && & 2 I am not sure I can solve all the problems. But just try.
send me your last version.
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E-mail： & QQ：8835100【交流】check cif网站有问题了？ - 晶体 - 小木虫 - 学术 科研 第一站
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【交流】check cif网站有问题了？
今天上午发现checkcif网站有问题了：
1.Calculated 和Reported 的晶体数据都没有显示
2.以前检测有问题（有错误的）的晶体数据，现在检测没有错误啊！
很奇观啊！
不知道 过来看看的 我也发现了！不知道怎么办!:tiger08: 今天中午开始有问题的， 是有问题了~~刚试了~~无奈中。。。:tuzi4::tuzi3: 可以给acta E&&主编写信呀通知呀
editors and co-editors of Acta Crystallographica Section E
editor-in-chief
G. Kostorz, ETH Zurich, Wolfgang-Pauli-Str. 16, CH-8093 Zurich, Switzerland(fax: +41-; e-mail: )
section editors
W. T. A. Harrison, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland (e-mail: )
J. Simpson, Department of Chemistry, University of Otago, PO Box 56, Dunedin, New Zealand (e-mail: )
M. Weil, Institute of Chemical Technologies and Analytics, Division of Structural Chemistry, Vienna University of Technology, Getreidemarkt 9/164-SC, Austria (e-mail: ) 是这样呀！支持个！ :(:tuzi11::tuzi11: 有问题了，如何办？ 刚才上了一下 现在网站貌似好了 可以用了 今天已经好了…… Thank you for your message. I apologise for the problem, caused by a system
upgrade. checkCIF should now work OK again.
Best wishes
Peter Strickland
----------------------------------------------------------------------
Peter Strickland, Managing Editor, IUCr Journals
IUCr Editorial Office, 5 Abbey Square, Chester CH1 2HU, England
Phone: 44 & &Fax: 44 & &Email:
Ftp: ftp.iucr.org& &WWW: http://journals.iucr.org/
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E-mail： & QQ：8835100【求助】cif 错误怎么改 - 晶体 - 小木虫 - 学术 科研 第一站
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【求助】cif 错误怎么改
PLAT232_ALERT_2_A Hirshfeld Test Diff (M-X)&&Pb4& & --&&N1_d& & ..& &&&112.49 su&&
PLAT230_ALERT_2_B Hirshfeld Test Diff for& & O5& &&&--&&C14& &&&..& && & 9.45 su& &
PLAT232_ALERT_2_B Hirshfeld Test Diff (M-X)&&Pb1& & --&&O13_a& &..& && &12.15 su& &
PLAT232_ALERT_2_B Hirshfeld Test Diff (M-X)&&Pb1& & --&&O15_d& &..& && &12.95 su& &
PLAT232_ALERT_2_B Hirshfeld Test Diff (M-X)&&Pb1& & --&&O3_e& & ..& && &10.25 su& &
PLAT232_ALERT_2_B Hirshfeld Test Diff (M-X)&&Pb4& & --&&O12& &&&..& && &11.58 su& &
PLAT232_ALERT_2_B Hirshfeld Test Diff (M-X)&&Pb4& & --&&O13_a& &..& && &21.19 su& &
PLAT232_ALERT_2_B Hirshfeld Test Diff (M-X)&&Pb4& & --&&O9_b& & ..& && &10.63 su& &
请高人指点一下
哈哈 :tiger05:
帮你顶一下 赶紧发吧
发完了请我吃饭 我也有类似的问题，顶一下 刚才试了EADP A B，解决了，你也不妨试试:D 键的刚性错误，试试
delu 0.01 atom1 atom2 由于你的数据不是很好导致的！ delu 0.01 atom1 atom2
simu 0.01 atom1 atom2
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E-mail： & QQ：8835100求高手帮我解决我的check cif - 晶体 - 小木虫 - 学术 科研 第一站
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求高手帮我解决我的check cif
checkCIF/PLATON report
Structure factors have been supplied for datablock(s) 1
THIS REPORT IS FOR GUIDANCE ONLY. IF USED AS PART OF A REVIEW PROCEDURE
FOR PUBLICATION, IT SHOULD NOT REPLACE THE EXPERTISE OF AN EXPERIENCED
CRYSTALLOGRAPHIC REFEREE.
No syntax errors found.& && &&&CIF dictionary& && &&&Interpreting this report
Datablock: 1
Bond precision:& & C-C = 0.0169 A Wavelength=0.71073
Cell: a=7.170(7) b=8.923(8) c=21.96(2)
alpha=90 beta=90 gamma=90
Temperature:&&296 K
Calculated Reported
Volume 05(2)
Space group& && && & P 21 21 21&&P2(1)2(1)2(
Hall group P 2ac 2ab&&?
Moiety formula& & C14 H16 Br N3 ?
Sum formula& && && & C14 H16 Br N3 C14 H16 Br N3
Mr 306.20 306.21
Dx,g cm-3 1.448 1.448
Mu (mm-1) 2.912 2.912
F000 624.0 624.0
F000' 623.04
h,k,lmax 9,12,29 9,12,29
Tmin,Tmax 0.434,0.497 0.475,0.542
Tmin' 0.401
Correction method= MULTI-SCAN
Data completeness= 1.65/0.95 Theta(max)= 28.660
R(reflections)= 0.) wR2(reflections)= 0.)
S = 4.331 Npar= 158
The following ALERTS were generated. Each ALERT has the format
& && & test-name_ALERT_alert-type_alert-level.
Click on the hyperlinks for more details of the test.
Alert level A
PLAT414_ALERT_2_A Short Intra D-H..H-X& && & H2& &&&..&&H12B& & ..& && & 1.43 Ang.&&
Alert level B
DIFMX01_ALERT_2_B&&The maximum difference density is & 0.1*ZMAX*1.00
& && && && &_refine_diff_density_max given =& && &4.596
& && && && &Test value =& && &3.500
GOODF01_ALERT_2_B&&The least squares goodness of fit parameter lies
& && && && &outside the range 0.60 && 4.00
& && && && &Goodness of fit given =& && &4.331
PLAT035_ALERT_1_B No _chemical_absolute_configuration info given .& &&&Please Do !
PLAT087_ALERT_2_B Unsatisfactory S value (Too High) ..............& && & 4.33& && &
PLAT094_ALERT_2_B Ratio of Maximum / Minimum Residual Density ....& && & 6.77& && &
PLAT097_ALERT_2_B Large Reported Max.&&(Positive) Residual Density& && & 4.60 eA-3&&
PLAT201_ALERT_2_B Isotropic non-H Atoms in Main Residue(s) .......& && && & 1 Why ?
PLAT341_ALERT_3_B Low Bond Precision on&&C-C Bonds ...............& &&&0.0169 Ang.&&
Alert level C
DIFMX02_ALERT_1_C&&The maximum difference density is & 0.1*ZMAX*0.75
& && && && &The relevant atom site should be identified.
RFACG01_ALERT_3_C&&The value of the R factor is & 0.10
& && && && &R factor given& &0.130
RFACR01_ALERT_3_C&&The value of the weighted R factor is & 0.25
& && && && &Weighted R factor given& &0.314
SHFSU01_ALERT_2_C&&The absolute value of parameter shift to su ratio & 0.05
& && && && &Absolute value of the parameter shift to su ratio given& &0.062
& && && && &Additional refinement cycles may be required.
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......& && &0.972& && &
PLAT080_ALERT_2_C Maximum Shift/Error ............................& && & 0.06& && &
PLAT082_ALERT_2_C High R1 Value ..................................& && & 0.13& && &
PLAT084_ALERT_3_C High wR2 Value (i.e. & 0.25) ...................& && & 0.31& && &
PLAT213_ALERT_2_C Atom C5& && && && &&&has ADP max/min Ratio .....& && &&&3.2 prolat
PLAT220_ALERT_2_C Large Non-Solvent& & C& &&&Ueq(max)/Ueq(min) ...& && &&&3.9 Ratio
PLAT220_ALERT_2_C Large Non-Solvent& & N& &&&Ueq(max)/Ueq(min) ...& && &&&3.6 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for& & N1& &&&--&&C5& && &..& && &&&5.8 su& &
PLAT230_ALERT_2_C Hirshfeld Test Diff for& & C1& &&&--&&C2& && &..& && &&&5.6 su& &
PLAT234_ALERT_4_C Large Hirshfeld Difference N3& &&&--&&C13& &&&..& && & 0.23 Ang.&&
PLAT234_ALERT_4_C Large Hirshfeld Difference C1& &&&--&&C9& && &..& && & 0.19 Ang.&&
PLAT234_ALERT_4_C Large Hirshfeld Difference C4& &&&--&&C5& && &..& && & 0.20 Ang.&&
PLAT234_ALERT_4_C Large Hirshfeld Difference C12& & --&&C14& &&&..& && & 0.22 Ang.&&
PLAT234_ALERT_4_C Large Hirshfeld Difference C13& & --&&C14& &&&..& && & 0.19 Ang.&&
PLAT241_ALERT_2_C High& && &Ueq as Compared to Neighbors for .....& && && &N3 Check
PLAT241_ALERT_2_C High& && &Ueq as Compared to Neighbors for .....& && &&&C13 Check
PLAT242_ALERT_2_C Low& && & Ueq as Compared to Neighbors for .....& && && &N1 Check
PLAT242_ALERT_2_C Low& && & Ueq as Compared to Neighbors for .....& && &&&C11 Check
PLAT242_ALERT_2_C Low& && & Ueq as Compared to Neighbors for .....& && &&&C12 Check
PLAT360_ALERT_2_C Short&&C(sp3)-C(sp3) Bond&&C12& & -& &C14& & ...& && & 1.39 Ang.&&
PLAT360_ALERT_2_C Short&&C(sp3)-C(sp3) Bond&&C13& & -& &C14& & ...& && & 1.36 Ang.&&
PLAT420_ALERT_2_C D-H Without Acceptor& && & N3& &&&-& &H12& & ...& &&&Please Check
Alert level G
PLAT003_ALERT_2_G Number of Uiso or Uij Restrained non-H Atoms ...& && && & 4& && &
PLAT005_ALERT_5_G No _iucr_refine_instructions_details&&in the CIF& &&&Please Do !
PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............& && && & 2 Why ?
PLAT335_ALERT_2_G Check Large C6 Ring& & C-C Range C1& &&&-C9& && && && &0.18 Ang.&&
PLAT791_ALERT_4_G The Model has Chirality at C11& && && & (Verify)& && && & R& && &
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............& && && &12 Note&&
& &1 ALERT level A = Most likely a serious problem - resolve or explain
& &8 ALERT level B = A potentially serious problem, consider carefully
&&26 ALERT level C = Check. Ensure it is not caused by an omission or oversight
& &6 ALERT level G = General information/check it is not something unexpected
& &2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
&&25 ALERT type 2 Indicator that the structure model may be wrong or deficient
& &6 ALERT type 3 Indicator that the structure quality may be low
& &6 ALERT type 4 Improvement, methodology, query or suggestion
& &2 ALERT type 5 Informative message, check
It is advisable to attempt to resolve as many as possible of the alerts in all categories. Often the
minor alerts point to easily fixed oversights, errors and omissions in your CIF or refinement
strategy, so attention to these fine details can be worthwhile. In order to resolve some of the more
serious problems it may be necessary to carry out additional measurements or structure
refinements. However, the purpose of your study may justify the reported deviations and the more
serious of these should normally be commented upon in the discussion or experimental section of a
paper or in the &special_details& fields of the CIF. checkCIF was carefully designed to identify
outliers and unusual parameters, but every test has its limitations and alerts that are not important
in a particular case may appear. Conversely, the absence of alerts does not guarantee there are no
aspects of the results needing attention. It is up to the individual to critically assess their own
results and, if necessary, seek expert advice.
Publication of your CIF in IUCr journals
A basic structural check has been run on your CIF. These basic checks will be run on all CIFs
submitted for publication in IUCr journals (Acta Crystallographica, Journal of Applied
Crystallography, Journal of Synchrotron Radiation); however, if you intend to submit to Acta
Crystallographica Section C or E, you should make sure that full publication checks are run on the
final version of your CIF prior to submission.
Publication of your CIF in other journals
Please refer to the Notes for Authors of the relevant journal for any special instructions relating to
CIF submission.
PLATON version of 18/09/2013; check.def file version of 12/09/2013
A类错误该怎么解决？
两个氢原子的位子加的有问题，可以用差值傅里叶重新加氢。 把原数据发上来，让别人帮你修 貌似原子认指和结构精修没有完成,
var cpro_id = 'u1216994';
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提供，小木虫为个人免费站点，仅提供交流平台，不对该内容负责。欢迎协助我们监督管理，共同维护互联网健康，如果您对该内容有异议，请立即发邮件到
联系通知管理员，也可以通过QQ周知，我们的QQ号为：8835100
我们保证在1个工作日内给予处理和答复，谢谢您的监督。
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欢迎监督，发现不妥请立即
E-mail： & QQ：8835100