Make This Publishable!
Joseph H. Reibenspies
Department of Chemistry
Texas A & M University
All rights are reserved. Please do not copy, modify or distribute these slideswithout the consent of the author
Notes ..
•On-line Lecture
–FLASH or HTML5 format (ISPRING)
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–Time : 45 mins
–Mistakes and errors
–Contact Joseph Reibenspies
–xray@tamu.edu
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•These lectures are intended for use for registered students of Texas A & MUniversity.
–Other students are welcome
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Are we done yet!?
•Degrees of doneness.
–Do You think it is done?
–Does the Boss think that it is done?
–Does the Editor think that it is done?
–Is it done?
Prof. Cotton’s Law.
“It is not done until it is published”
Law of Diminishing Returns
•I think it is done when the effortI put into the structure farexceeds the quality of resultsthat is returned.
•A Boss thinks that it is donewhen the effort put into thestructure meets or exceeds theprojects expectations.
•The Editor thinks that is donewhen the effort put into thestructure meets or exceeds thepublication standard.
Quality of Results
Effort
The CIF file
•Crystallographic Information File
–Hall, Allen, Brown Acta Cryst. 1991 A47 655-685
–ASCI file
•80 characters/line
•Variables _nom
–Value for variable appears after variable name or on next line.
–Values can be contained by quotations
–Values more than one line long are contained by semicolons
•List of values can be initiated by a command loop
–Loop_
CIF generation and CheckCIF
•CIF generated by SHELXL/ACTA
•XCIF, OLEX2, CIFIX
–Extracts information from *.pcf (sad.abs) file andmodifies the CIF file.
•checkcif.iucr.org
–Reads the CIF (FCF) file and runs structurevalidation routines.
CheckCIF
CheckCIF - ALERTS
test-name_ALERT_alert-type_alert-level Format : test-name_ALERT_alert-type_alert-level.
ALERT level A = Most likely a serious problem - resolve or explain
ALERT level B = A potentially serious problem, consider carefully
ALERT level C = Check. Ensure it is not caused by an omission or oversight
ALERT level G = General information/check it is not something unexpected
ALERT type 1 CIF construction/syntax error, inconsistent or missing data
ALERT type 2 Indicator that the structure model may be wrong or deficient
ALERT type 3 Indicator that the structure quality may be low
ALERT type 4 Improvement, methodology, query or suggestion
ALERT type 5 Informative message, check
PLAT052_ALERT_1_B Info on Absorption Correction Method Missing ... ?
level : Serious : Action needed!
CIF error - Missing data : Replace ? in CIF with : multi-scan (SADABS)CIF error - Missing data : Replace ? in CIF with : multi-scan (SADABS)
PLAT230_ALERT_2_B Hirshfeld Test Diff for C7 -- C8 .. 7.5 su
level : Serious : Action needed!
Problem with structure (see next slide)Problem with structure (see next slide)
PLAT007_ALERT_5_G Note: Number of Unrefined D-H Atoms ............ 2
level : Not Serious : No Action needed, All hydrogen atoms were constrained to riding model
It is standard practice to refine Hydrogen atoms on hetero atoms as proof of their correct assignment
Example
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Hirshfeld rigid bond test*
•Two bonded atoms vibrate along the bondwith approximately equal amplitude.
•Those which deviate more than a few su unitsneed attention.
*Hirshfeld (1976) Acta Cryst. A32, 239-244.
Inspect the ORTEP
12/4/2012
DRAFT
11
Ellipsoid problems
Wrong Atom assignment
Missing Atom
Disorder
Vibration
(Dynamic Disorder)
absorption
Hg
X
“Error Sumps”
Inspect the E maps
12/4/2012
DRAFT
13
Fix it, Fix it, Fix it ..
2-fold
3-fold
4-fold
Not Fixed yet …
Still too large
FragmentDisorder
Allow movementof pivot carbon
The effort
SAME_TBU .005 O1 > C14SAME_TBU .005 O1 > C14
SIMU_TBU .005 O1 > C14SIMU_TBU .005 O1 > C14
DELU_TBU .005 O1 > C14DELU_TBU .005 O1 > C14
WGHT 0.081600 0.384700WGHT 0.081600 0.384700
FVAR 0.17173 0.86470FVAR 0.17173 0.86470
RESI 1 TBURESI 1 TBU
PART 1PART 1
O1 3 0.579881 0.110527 0.314546 21.00000 0.03575O1 3 0.579881 0.110527 0.314546 21.00000 0.03575
AFIX 147AFIX 147
H1 2 0.585410 0.054695 0.288414 21.00000 -1.50000H1 2 0.585410 0.054695 0.288414 21.00000 -1.50000
AFIX 0AFIX 0
C1 1 0.454675 0.132022 0.376560 21.00000 0.02916C1 1 0.454675 0.132022 0.376560 21.00000 0.02916
......
C14 1 0.080292 0.128310 0.662195 21.00000 0.06102C14 1 0.080292 0.128310 0.662195 21.00000 0.06102
RESI 2 TBURESI 2 TBU
PART 2PART 2
O1 3 0.219774 -0.015070 0.504861 -21.00000 0.05166O1 3 0.219774 -0.015070 0.504861 -21.00000 0.05166
AFIX 147 AFIX 147
H1 2 0.279100 -0.070661 0.486339 -21.00000 -0.02379H1 2 0.279100 -0.070661 0.486339 -21.00000 -0.02379
AFIX 0AFIX 0
C1 1 0.280204 0.071108 0.481746 -21.00000 0.03749C1 1 0.280204 0.071108 0.481746 -21.00000 0.03749
......
C14 1 0.350292 0.445652 0.368532 -21.00000 0.06632C14 1 0.350292 0.445652 0.368532 -21.00000 0.06632
_diffrn_reflns_number 20110
_refine_ls_number_reflns 8191
_refine_ls_number_parameters 518
_refine_ls_number_restraints 297
Data to Parameter Ratio15.81
Finally …
2-fold 2-Fragment
Disorder
Data to Parameter Ratio
0.0
10.0
20.0
Theoretical
Scientist
Experimental
Scientist
“Lower Limit”
No disorder
model
2-fold disordered
tBu model
2-fold disordered
Frag model
Over-modeling
2-fold disordered
2 Frag model
If you can’t fix it ….
•If you can’t fix it at least explain the problem.
–Disorder
–Bad, weak or incomplete data
–Twinning
–Etc..
•Cover Letter (ok)
•CIF (best)
–Validation Response Form
Validation Response Form
The Validation Response Form (VRF) is a portion of text in CIF format supplied in thecheckCIF report that indicates the problems that have triggered Alerts at level A or B
The completed VRF should be inserted in the CIF after the first datablock identifier(data_datacode)
_vrf_errorcode_datacode
;
PROBLEM: text from checkCIF
RESPONSE: Your reply or see _publ_section_exptl_refinement
;
For IUCR journals it is preferable for explanatory text to be placed in the relevant fields in the CIFsuch as _publ_section_exptl_refinement.
EXAMPLE :
data_structure1
_vrf_PLAT213_structure1
;
PROBLEM: Atom C(6B) has ADP max/min ratio ............ 5.20
RESPONSE: Atom C6 of the ring (B) was found to be disordered
;
Wrap it up
•Catch problems before the reviewers do
•Be honest and forthcoming
–If you don’t know say so
–No masking or hiding a problem
•Do not overdo it
–Keep your structure simple (as you can)
•Always include the data
–Let someone else help
How do you learn more?
•Books ..
–“Crystal Structure Determination”
•Werner Massa : ISBN-10: 3540206442
–“Crystal Structure Analysis: Principles and Practice ”
•William Clegg : ISBN-10: 0199219478
–“Crystal Structure Refinement: a crystallographer’s guide to SHELXL”
•ed. Peter Müller. : ISBN-10: 0198570767
•On – line ..
–xray.tamu.edu/courses …
•Eight full lectures for Single-Crystal
•Eight full lectures for Powder Diffraction