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小木虫论坛-学术科研互动平台 » 材料区 » 晶体 » 晶体解析 » 【求助】10金币求加氢键
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lipan504

铁杆木虫 (著名写手)

[交流] 【求助】10金币求加氢键

本人是解单晶初学者，想对我的数据加氢键，自己用汞软件加氢，测量后发现如下A类错误，望有高人出现。不知传个cif文件够不够。附件中有cif文件和A类错误。急。。。同时希望虫友能“授我于鱼，更能授我于渔”谢谢各位虫友！
附件如下：
cif文件：
http://www.namipan.com/d/100924g ... 598ee4be019d6660000
错误：
http://www.namipan.com/d/checkCI ... 3e68de6d992ed310000
10金币求加氢键
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1楼2010-12-14 10:41:57
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ljmmarise

至尊木虫 (著名写手)
lipan504(金币+1): 2010-12-14 11:51:39
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A

c3 H3 O4  0.93   2.51   3.342(5)  149 2_867
。。。。。

自己按照这样的格式编辑在cif文件的“_diffrn_measured_fraction_theta_max    0.981
_diffrn_reflns_theta_full              25.02
_diffrn_measured_fraction_theta_full   0.981
_refine_diff_density_max    0.409
_refine_diff_density_min   -0.297
_refine_diff_density_rms    0.074


#=====================  End of CIF submission ===========================”前面
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8楼2010-12-14 11:48:52
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ljmmarise

至尊木虫 (著名写手)
lipan504(金币+1): 2010-12-14 11:25:13
checkCIF/PLATON report (publication check)
No syntax errors found.                               CIF dictionaryPlease wait while processing ....                     Interpreting this reportDatablock: 100924g
--------------------------------------------------------------------------------
Bond precision: C-C = 0.0070 A Wavelength=0.71073
Cell: a=5.3521(5) b=15.5146(16) c=15.5615(14)
alpha=114.351(2) beta=95.145(1) gamma=97.072(1)
Temperature:  298 K   
Calculated Reported
Volume 1154.07(19)  1154.07(19)
Space group P -1  P-1  
Hall group -P 1  -P1  
Moiety formula C22 H16 F3 N O7 S  C F3 O2 S,C15 H11 N O4,C6 H5 O  
Sum formula C22 H16 F3 N O7 S  C22 H16 F3 N O7 S  
Mr 495.43 495.42  
Dx,g cm-3 1.426 1.426  
Z 2 2  
Mu (mm-1) 0.207 0.207  
F000 508.0 508.0
F000' 508.60   
h,k,lmax 6,18,18 6,18,18
Nref 4085  4008  
Tmin,Tmax 0.921,0.961 0.913,0.962
Tmin' 0.911  
Correction method= MULTI-SCAN  
Data completeness= 0.981 Theta(max)= 25.020
R(reflections)= 0.0660( 2079) wR2(reflections)= 0.1627( 4008)
S = 1.001 Npar= 312

--------------------------------------------------------------------------------

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
PLAT726_ALERT_2_A H...A   Calc     8.92000, Rep     2.48000 Dev...       6.44 Ang.
              H15A -O2      1.555   1.555                    #         55      
PLAT726_ALERT_2_A H...A   Calc     4.21000, Rep     2.53700 Dev...       1.67 Ang.
              H13A -O7      1.555   1.555                    #         55      
PLAT707_ALERT_1_A D...A   Calc    8.565(5), Rep    3.201(6), Dev..    1072.80 Sigma
              C15  -O2      1.555   1.555                    #         55      
PLAT707_ALERT_1_A D...A   Calc     3.72(3), Rep    3.404(3), Dev..      10.53 Sigma
              C13  -O7      1.555   1.555                    #         55      
PLAT728_ALERT_1_A D-H..A  Calc       66.00, Rep      131.03 Dev...      65.03 Deg.
              C15  -H15A -O2      1.555   1.555   1.555      #         99      
PLAT728_ALERT_1_A D-H..A  Calc       54.00, Rep      148.77 Dev...      94.77 Deg.
              C13  -H13A -O7      1.555   1.555   1.555      #         99      
--------------------------------------------------------------------------------Alert level B
PLAT242_ALERT_2_B Check Low       Ueq as Compared to Neighbors for        C14     
PLAT242_ALERT_2_B Check Low       Ueq as Compared to Neighbors for        C17     
PLAT601_ALERT_2_B Structure Contains Solvent Accessible VOIDS of .     108.00 A**3
--------------------------------------------------------------------------------Alert level C
PLAT220_ALERT_2_C Large Non-Solvent    C     Ueq(max)/Ueq(min) ...       3.06 Ratio
PLAT230_ALERT_2_C Hirshfeld Test Diff for    N1     --  C1      ..       5.11 su   
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for         O5     
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C19     
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C21     
PLAT241_ALERT_2_C Check High      Ueq as Compared to Neighbors for        C22     
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C20     
PLAT331_ALERT_2_C Small Average Phenyl   C-C Dist. C17    -C22           1.36 Ang.
PLAT340_ALERT_3_C Low Bond Precision on  C-C Bonds (x 1000) Ang ..          7      
PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings  Differ          ?
--------------------------------------------------------------------------------Alert level G
PLAT301_ALERT_3_G Note: Main Residue  Disorder ...................       3.00 Perc.
PLAT779_ALERT_4_G Suspect or Irrelevant (Bond) Angle in CIF .... #         64     
              O7   -C16  -O7'     1.555   1.555   1.555             44.00 Deg.
PLAT793_ALERT_4_G The Model has Chirality at C8      (Verify) ....          S      
PLAT793_ALERT_4_G The Model has Chirality at C9      (Verify) ....          S      
PLAT793_ALERT_4_G The Model has Chirality at C12     (Verify) ....          S      
--------------------------------------------------------------------------------   6 ALERT level A = In general: serious problem
   3 ALERT level B = Potentially serious problem
  10 ALERT level C = Check and explain
   5 ALERT level G = General alerts; check

   5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
  13 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
Publication of your CIF
You should always 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 nature of your study may justify the reported deviations from the submission requirements of the journal and these should be commented upon in the discussion or experimental section of a paper - after all, they might represent an interesting feature.

If level A alerts remain, which you believe to be justified deviations, and you intend to submit this CIF for publication in Acta Crystallographica Section C or Section E, you should additionally insert an explanation in your CIF using the Validation Reply Form (VRF) below. Your explanation will be considered as part of the review process.

If you intend to submit to another section of Acta Crystallographica or Journal of Applied Crystallography or Journal of Synchrotron Radiation, you should make sure that at least a basic structural check is run on the final version of your CIF prior to submission.


# start Validation Reply Form
_vrf_PLAT726_100924g
;
PROBLEM: H...A   Calc     8.92000, Rep     2.48000 Dev...       6.44 Ang.
RESPONSE: ...
;
_vrf_PLAT707_100924g
;
PROBLEM: D...A   Calc    8.565(5), Rep    3.201(6), Dev..    1072.80 Sigma
RESPONSE: ...
;
_vrf_PLAT728_100924g
;
PROBLEM: D-H..A  Calc       66.00, Rep      131.03 Dev...      65.03 Deg.
RESPONSE: ...
;
# end Validation Reply FormIf you wish to submit your CIF for publication in Acta Crystallographica Section C or E, you should upload your CIF via the web. If your CIF is to form part of a submission to another IUCr journal, you will be asked, either during electronic submission or by the Co-editor handling your paper, to upload your CIF via our web site.  

--------------------------------------------------------------------------------
PLATON version of 22/10/2010; check.def file version of 11/10/2010 Datablock 100924g - ellipsoid plot
  

--------------------------------------------------------------------------------
Download CIF editor (publCIF) from the IUCr
Download CIF editor (enCIFer) from the CCDC
Test a new CIF entry


你氢键的对称操作码有问题
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2楼2010-12-14 11:17:22
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lipan504

铁杆木虫 (著名写手)
引用回帖:
Originally posted by ljmmarise at 2010-12-14 11:17:22:
checkCIF/PLATON report (publication check)
No syntax errors found.                               CIF dictionaryPlease wait while processing ....                     Interpreting this reportDatabl ...

ljmmarise  
能否先帮我改改，然后再我怎么改啊！在下感激不尽！
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3楼2010-12-14 11:26:14
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ljmmarise

至尊木虫 (著名写手)
你的氢键列表要重新搞一个
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4楼2010-12-14 11:31:46
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