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lipan504

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[交流] 【求助】10金幣求加氫鍵

本人是解單晶初學(xué)者，想對(duì)我的數(shù)據(jù)加氫鍵，自己用汞軟件加氫，測量后發(fā)現(xiàn)如下A類錯(cuò)誤，望有高人出現(xiàn)。不知傳個(gè)cif文件夠不夠。附件中有cif文件和A類錯(cuò)誤。急。。。同時(shí)希望蟲友能“授我于魚，更能授我于漁”謝謝各位蟲友！
附件如下：
cif文件：
http://www.namipan.com/d/100924g ... 598ee4be019d6660000
錯(cuò)誤：
http://www.namipan.com/d/checkCI ... 3e68de6d992ed310000
10金幣求加氫鍵

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為什么cif后面加上氫鍵信息會(huì)出現(xiàn)A類錯(cuò)誤已經(jīng)有3人回復(fù)
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1樓 2010-12-14 10:41:57

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ljmmarise

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lipan504(金幣+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

你氫鍵的對(duì)稱操作碼有問題

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2樓2010-12-14 11:17:22

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lipan504

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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
能否先幫我改改，然后再我怎么改�。≡谙赂屑げ槐M！

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3樓2010-12-14 11:26:14

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ljmmarise

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你的氫鍵列表要重新搞一個(gè)

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4樓2010-12-14 11:31:46

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ljmmarise

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(Analysis of Potential Hydrogen Bonds and Schemes with d\(D...A\) < R\(D\)+R\(A\)+0.50, d\(H...A\) < R\(H\)+R\(A\)-0.12 Ang., D-H...A > 100.0 Deg)s
(====================================================================================================================================)s
(Note: - ARU codes in [] are with reference to the Coordinates printed above \(Possibly transformed, when MOVE .NE. 1.555\))s
(====================================================================================================================================)s
( )s
(Nr Typ Res Donor --- H....Acceptor [ ARU  ]    D - H    H...A    D...A  D - H...A A..H..A* A'..H..A" Sum\(XY,YZ\)  Sum\(XZ\))s
(------------------------------------------------------------------------------------------------------------------------------------)s
( )s
( 1    1 C\(3\)  --H\(3\) ..O\(4\) [  2867.01]    0.93    2.51 3.342\(5\)       149)s
( 2 Intra 1 C\(12\) --H\(12\)  ..O\(7'\)  [       ]    0.98    2.30 2.688\(8\)       103)s
( 3    1 C\(15\) --H\(15A\) ..O\(2\) [  2767.01]    0.97    2.48 3.201\(6\)       131)s
( 4 Intra 1 C\(18\) --H\(18\)  ..O\(6\) [       ]    0.93    2.42 2.740\(6\)       100)s
( )s
(:: No Classic Hydrogen Bonds Found)s
( )s
( )s
(Translation of ARU-code to Equivalent Position Code)s
(===================================================)s
( [  2767. ]  = 2-x,1-y,2-z)s
( [  2867. ]  = 3-x,1-y,2-z)s

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5樓2010-12-14 11:33:22

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lipan504

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引用回帖:

Originally posted by ljmmarise at 2010-12-14 11:31:46:
你的氫鍵列表要重新搞一個(gè)

現(xiàn)在能幫我弄一下不？？

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6樓2010-12-14 11:33:32

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lipan504

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引用回帖:

Originally posted by ljmmarise at 2010-12-14 11:33:22:
(Analysis of Potential Hydrogen Bonds and Schemes with d\(D...A\) < R\(D\)+R\(A\)+0.50, d\(H...A\) < R\(H\)+R\(A\)-0.12 Ang., D-H...A > 100.0 Deg)s
(====================================== ...

能否弄成word 或txt格式發(fā)給我啊
上傳到納米盤吧

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7樓2010-12-14 11:36:18

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ljmmarise

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lipan504(金幣+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
。。。。。

自己按照這樣的格式編輯在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樓2010-12-14 11:48:52

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lipan504

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引用回帖:

高人，按你說的修改還是一樣出現(xiàn)錯(cuò)誤了！再幫忙看看好么？

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9樓2010-12-14 11:50:19

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lipan504

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引用回帖:

Originally posted by ljmmarise at 2010-12-14 11:48:52:
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_hb ...

checkcifplaton還是有錯(cuò)誤�。�

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10樓2010-12-14 11:52:19

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[考博] 26申博 +4	八6八68 2026-03-16	4/200	2026-03-17 13:00 by 輕松不少隨
[考研] 藥學(xué)383 求調(diào)劑 +3	藥學(xué)chy 2026-03-15	4/200	2026-03-16 20:51 by 元子^0^
[考研] 304求調(diào)劑 +3	曼殊2266 2026-03-14	3/150	2026-03-16 16:39 by houyaoxu
[考研] 求老師收留調(diào)劑 +4	jiang姜66 2026-03-14	5/250	2026-03-15 20:11 by Winj1e
[考研] 289求調(diào)劑 +4	這么名字咋樣 2026-03-14	6/300	2026-03-14 18:58 by userper

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