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W i n g x   T u t o r


S T A G E   I


ü Step 1 : Have NV10.ins, NV10.hkl in a folder

ü Step 2 : Launch Wingx

ü Step 3 : File → change project → select new project →

Click (a new window opens)

ü Step 4: In the new window using Browse select the NV10.hkl file press OK we will get a crystal data like axes, angles etc.

ü Step 5 : Refine → open INS file  ( examine this INS file for its completeness)

ü Step 6 : Solve → SHELXS – 97 → click

ü Step 7   : press OK in control panel a new window opens in which appropriate solution is found.

Note: The values of RE and Number of atom

        Ex: RE = 0.211 for 19 atoms and 366 E- values

ü Step 8 : Close this window now NV10.res is created in addition to SHELXS.lst and two more files

ü Step 9  : Close the Window ( use solve instruction only once)

ü Step 10   : Refine → open Res file

ü Step 11 : Change Q→ (Replace) C and then O without changing the numbers. Delete unwanted Q’s below.

ü Step 12  : Change the atom sequence number C = 1, O = 3, S = 4, Br = 5

ü Step 13   : File → Save as INS, close the box (Window)

 

S T A G E  I I ( First Refinement) (Isotropic)

ü Step 14   : Refine → SHELXL – 97 → click see the R1 factor it will be between .15 and .25 normally (for small structure)

ü Step 15       : Click on SHELX Graphical model editor  then we get a green window.

ü Step 16       : Get the SXGRAPH window which displays the structure found by the program, this structure is not exact we have to refine again and again by locating the atoms (White dots) and renaming them into the required atoms seeing the chemical diagram.

 

 

ü Step 17       : On the right side of graph display Q-peaks remove tick (√ mark) now rotate the structure and try to bring the required structure by renaming the Q – Peaks  part by part.

üStep 18       : Click  yellow → right click  ( change atom properties)

ü Step 19     : Label atoms (click) for view name (like C12, C13)

ü Step 20     : For delete atom → delete → selected atom

ü Step 21     : Save INS file → close the window

ü Step 22     : Refine → SHELXL – 97

ü Step 23     : SXGRAPH see corrected and save INS ( see Refine → SHELXL value of R1→reduced to .1001 from .1801

ü Step 24     : Rename atom names in anticlockwise direction.

ü Step 25     : Save INS file. Close the window

ü Step 26     : Refine → SHELXL – 97

S T A G E  I I I (ANISOTROPIC REFINEMENT)

ü Step 27     : Add ANIS Instruction before first atom

ü Step 28     : Save as INS

ü Step 29     : Refine → SHELXL – 97

S T A G E  I V ( ADDING HYDROGEN)

ü Step 30     : HFIX 43 C2 Adds one hydrogen to a ring carbon C2 this instruction should be added previous to the C2 atom coordinates in the RES file

ü Step 31     : save as INS→ Refine SHELXL – 97

Note           : HFIX 43  → ring carbon with 1 hydrogen

                   : HFIX 137→ to add 3 hydrogen’s

                   : HFIX 23→ to add 2 Hydrogen’s


                   : HFIX 13 → to add 1 hydrogen in ring with

 another atom ex:

                   : HFIX 147 O1→ add one hydrogen to O1

                   : HFIX 83 S1→ add one hydrogen to S1

: HFIX 93 → to fix hydrogen in Terminal  Nitrogen

: Terminal NH2 HFIX 93

ü Step 32     : WGHT (Ctrl + X cut the WGHT instruction in the bottom of the program) and Replace with the upper WGHT instruction of the program.

ü Step 33     : GooF Goodness of Fit it should be 1.00 (good) or near to 1 

ORTEP DIAGRAM:

ü Label → Labeling mode  → No Labels  → Click

ü Label  → Set mouse labels  → left click  → Fix Right click → Print Screen  → Invert colour

(or)

ü using GS view software: ortep file menu → write postscript file → color (click) then goto to source folder you can see .EPS file (open it using GS VIEW software)

AFTER SOLVING STRUCTURE:

ü Before Bond

ACTA (Delete OMIT)

conf

Temp 20

Size 0.2 0.15 0.18

We can see CIF, FCF two files

PLATON

ü Select .Res file

ü Click  third icon platon graphic menu

PLUTON

ü
Click pluton auto

ü
Contents    Unit cell box click

ü
Pack range       

ü
View    View normal to (1 0 0)

   (0 1 0)

                                           (0 0 1)

ü Graphic     pluton    Pack

ü
ARU     Assymmetric residual unit (label ARU)

ü Delete Single structure “Exclude ARU”

ü To remove Box – Unit cell box

ü Pack range: Don’t remove small values (ex:1555) and remove (ex: 4555)

PLATON

ü
Publish    Calcall (example: ani.lis) ( it creates a .Lis file)

Note: S=1, HP=.6,.7, R= <0.08 Rall = <0.08

.RES COMMANDS

CELL -- Wavelength followed by unit cell dimensions. The wavelength has no importance in this calculation.

ZERR -- Number of asymmetric units in the unit cell, followed by estimated errors in the unit cell dimensions. Estimates do not have to be accurate.

LATT -- Primitive is "-1", C centered is "-7", I centered is "-2", F centered is "-4". The negative sign indicates that the structure is non-centrosymmetric.

SYMM -- Symmetry operators. The operator X,Y,Z is always assumed, so may NOT be input. If your structure is C, I, or F centered, do not put the lattice centering operators. These operators are specified by the choice of LATT, above. See this list of symmetry operators for your space group.

SFAC -- The element symbol defining the heavy atom. The first 94 elements of the periodic table are recognized.

UNIT -- The number of heavy atom in the cell. A ball park figure, can be larger than what you expect.

PATS -- Generates starting atoms consistent with Patterson. It is "slightly" better than starting from random positions.

FIND -- Number of atoms to find. Just a guess.

NTRY -- Number of trials. If not specified, the program will run forever. I have found that if you don't get a decent answer in 50 trials, you will probably never get it. Find a better derivative.

MIND -- The shortest distance allowed between atoms for PATS and FIND. Here it is set to 3 Angstroms since it is unlikely that two heavy atom sites would be closer than this. The negative sign is used as a flag to output a crossword table in the log file. The crossword table is important for judging the quality of the solution. Keep MIND negative.

SHEL -- Resolution limits.

HKLF -- Set it to 3 for F or FA or deltaF (e.g. output from xprep). Set it to 4 for F2 in .hkl file. 

Data validation prefilter

PUBLICATION MATERIAL

PUBL_001,PUBL_002
PUBL_003,PUBL_004
TYPE_001,TYPE_002

_publ_contact_author_name
_publ_contact_author_address

These must be present and must be of type char, although the old
_publ_contact_author is still allowed.

PUBL_005,TYPE_003

_publ_contact_author_email
_publ_contact_author_fax
_publ_contact_author_phone

email must be of type char.

PUBL_006,TYPE_006

_publ_requested_journal

Must be present and must be of type char.

PUBL_008,TYPE_008

_publ_section_title

Must be present and must be of type char.

PUBL_009,TYPE_009

_publ_author_name

Must be present and must be of type char.

PUBL_010,TYPE_010

_publ_author_address

Must be present and must be of type char.

PUBL_011,TYPE_011

_publ_section_synopsis

If present must be of type char.

PUBL_012,TYPE_012

_publ_section_abstract

Must be present and must be of type char.

PUBL_013,TYPE_013

_publ_section_comment

If present must be of type char.

PUBL_014,TYPE_014

_publ_section_exptl_prep

If present must be of type char.

PUBL_016

_publ_section_exptl_refinement
_computing_data_collection
_computing_cell_refinement
_computing_data_reduction
_computing_structure_solution
_computing_structure_refinement
_computing_molecular_graphics
_computing_publication_material

At least one of these must be present to give details of the refinement.
All of these must be of type char if they are present.

PUBL_017

_publ_section_references

Should be present and not empty.

PUBL_018,PUBL_019,
PUBL_020,PUBL_021

_publ_contact_author_name
_publ_contact_author_address

This test has failed due to what is probably an incorrectly formatted
author/address loop. Usual errors encountered in this loop are due to an
incorrect number of elements being given in the loop, or misuse of ;
(semi-colon) delimiters in order to get the CIF to pass checkCIF. If there
are no footnotes to be included in the author/address loop then the loop
should have the form as below,

loop_
_publ_author_name
_publ_author_address
'Bowes, Katharine F.' # Format is 'Surname, Firstnames'
;
School of Chemistry
University of St Andrews
St Andrews
Fife KY16 9ST
Scotland
;

'Ferguson, George'
; Department of Chemistry
University of Guelph
Guelph
Ontario
Canada N1G 2W1
;


When footnotes are required, then the format is as below. Note the use of . as
a placeholder for entries not requiring a footnote.

loop_
_publ_author_name
_publ_author_footnote
_publ_author_address
'Bowes, Katharine F.' . # Note . as placeholder
;
School of Chemistry
University of St Andrews
St Andrews
Fife KY16 9ST
Scotland
;

'Ferguson, George'
;
Permanent address: Department of Chemistry
University of Guelph
Guelph
Ontario
Canada N1G 2W1
;
;
School of Chemistry
University of St Andrews
St Andrews
Fife KY16 9ST
Scotland
;

'Lough, Alan J.' .
;
Lash Miller Chemical Laboratories
University of Toronto
Toronto
Ontario
Canada M5S 3H6
;

PUBL_024

 

Large number of authors.

The number of authors is greater than 6. Please specify the
role of each of the co-authors for your paper.

The co-authors of a paper should be all those who have made
significant scientific contributions to the work reported and
who share responsibility and accountability for the results.
An administrative, or similar, relationship to the work does
not of itself qualify a person for co-authorship.
/td>

PUBL_022

 

Mismatched subscript operators.

A line has been found with mismatched subscript operators(~).
If you require a single ~ (tilde) then this must be escaped with a .
e.g. the time taken was ~ 3 seconds.
Otherwise there should be pairs of matching ~, e.g. C~3~H~8~O
which would signify C3H8O.

PUBL_023

 

Mismatched superscript operators.

A line has been found with mismatched superscript operators(^).
If you require a single ^ (caret) then this must be escaped with a . i.e. ^
Otherwise there should be pairs of matching ^, e.g. ^12^C
which would signify 12C.

PUBL_025

_publ_section_comment

_publ_section_comment is more than 400 words.
For Acta Crystallographica Section E the Comment section
is usually expected to be no more than 400 words. Please
shorten your Comment if you intend to submit to Section E.
This limit does not apply to Acta Crystallographica Section C.

PUBL_026

_publ_section_comment

_publ_section_comment is less than 200 words.
For Acta Crystallographica Section C the Comment section
is usually expected to be longer than 200 words. Please
refer to the Notes for Authors for more details.

ATOM_001

_atom_type_scat_source

Must be present and must be of type char.

     

DATA SPECIFIC TO A GIVEN STRUCTURE

CHEM_001,TYPE_015

_chemical_formula_sum

Must be present and of type char.

CHEM_002,TYPE_016

_chemical_formula_moiety

If present must be of type char.

CHEM_003,TYPE_017

_chemical_formula_weight

Must be present and of type numb.

SYMM_001

_symmetry_cell_setting

Must be present and of type char.

SYMM_003,TYPE_018

_symmetry_space_group_name_H-M

Must be present and of type char.

SYMM_004,SYMM_005
TYPE_201

_symmetry_equiv_pos_as_xyz

Must be present and of type char. Also must not contain fractions
as decimals. e.g. 'x+0.5,y+0.5,z' is not allowed.
'x+1/2,y+1/2,z' is OK.

CELL_211-213,CELL_221-226
CELL_231-233,CELL_241-242
CELL_251-255,CELL_261-264
CELL_271-273
TYPE_019-024

_cell_length_a
_cell_length_b
_cell_length_c
_cell_angle_alpha
_cell_angle_beta
_cell_angle_gamma

All should be of type numb. _cell_length_a must always be present.
A check is made against the cell setting to ensure that all the required
information is given

CELL_001,TYPE_025

_cell_volume

Must be present and of type numb.

CELL_002,TYPE_026

_cell_formula_units_Z

Must be present and of type numb.

EXPT_001,TYPE_027

_exptl_crystal_density_diffrn

Must be present (not powder) and of type numb.

EXPT_002,EXPT_003
TYPE_028,TYPE_029

_exptl_crystal_density_meas
_exptl_crystal_density_method

A value must be present if a method given and vice versa.
Method must be type char.

DIFF_001,DIFF_101
DIFF_102,TYPE_030

_diffrn_radiation_type

Must be present and of type char.

DIFF_002,TYPE_031

_diffrn_radiation_wavelength

Must be present and of type numb.

CELL_003,TYPE_032

_cell_measurement_reflns_used

Must be present (not area/powder) and a number.

CELL_004,CELL_005
CELL_101
TYPE_033,TYPE_034

_cell_measurement_theta_min
_cell_measurement_theta_max

Must be present (not area/powder) and of type numb.

CELL_006,TYPE_035

_cell_measurement_temperature

Must be present and of type numb.

EXPT_004,TYPE_036

_exptl_absorpt_coefficient_mu

Must be present (not powder) and of type numb.

EXPT_005,TYPE_037

_exptl_crystal_description

Must be present (not powder) and be of type char.

EXPT_006,TYPE_038
EXPT_007,TYPE_138
EXPT_008,TYPE_238
EXPT_108,TYPE_338

_exptl_crystal_size_max
_exptl_crystal_size_mid
_exptl_crystal_size_min
_exptl_crystal_size_rad

Must be numbers, in order. (not required for powder papers)
_rad should be present for cylinder/sphere.

EXPT_010,TYPE_039
EXPT_110,EXPT_111
EXPT_112

_exptl_crystal_colour

Must be present and of type char.

DIFF_003,DIFF_004
TYPE_041,TYPE_042

_diffrn_measurement_device_type
_diffrn_measurement_device

(old)

Must be present and of type char.

DIFF_005,TYPE_043

_diffrn_measurement_method

Must be present (not powder) and of type char.

DIFF_006,TYPE_044

_diffrn_detector_area_resol_mean

Must be a number and should be present for area detector papers.

EXPT_011,EXPT_101
EXPT_102,EXPT_103
TYPE_045,TYPE_046
EXPT_013,TYPE_047
EXPT_014,TYPE_048

_exptl_absorpt_correction_type
_exptl_absorpt_process_details
_exptl_absorpt_correction_T_min
_exptl_absorpt_correction_T_max

Must be recognised (default is none). (not area)
_type must be present if Tmin/Tmax present.
Tmin/Tmax must be numbers. Must be present
if _type present and not none.

DIFF_007,TYPE_049

_diffrn_reflns_number

Must be present (not powder) and a number.

REFL_001,TYPE_050

_reflns_number_total

Must be present (not powder) and a number.

REFL_002,TYPE_051
REFL_003,TYPE_052

_reflns_number_gt
_reflns_number_observed

(old)

Must be present (not powder) and a number.

REFL_004,TYPE_053
REFL_005,TYPE_054

_reflns_threshold_expression
_reflns_observed_criterion

(old)

Must be present (not powder) and of type char.

DIFF_008,TYPE_055

_diffrn_reflns_theta_max

Must be present (not powder) and of type numb.

DIFF_012,TYPE_059

_diffrn_reflns_av_R_equivalents

(Not area/powder) Must be a number, must be present if
_reflns_number_total not equal to _reflns_number_gt
(or _observed). Must be zero if present and _total = _gt.

DIFF_013,TYPE_060
DIFF_014,TYPE_061
DIFF_015,TYPE_062
DIFF_016,TYPE_063
DIFF_017,TYPE_064
DIFF_018,TYPE_065

_diffrn_reflns_limit_h_min
_diffrn_reflns_limit_h_max
_diffrn_reflns_limit_k_min
_diffrn_reflns_limit_k_max
_diffrn_reflns_limit_l_min
_diffrn_reflns_limit_l_max

Must be present (not powder) and numbers.

DIFF_019,TYPE_066

_diffrn_standards_number

Must be present (not area/powder) and a number.

DIFF_020
TYPE_067,TYPE_068

_diffrn_standards_interval_count
_diffrn_standards_interval_time

One of these must be present (not area/powder)
and must be numbers.

DIFF_022,TYPE_069

_diffrn_standards_decay_%

Must be present (not powder) and a number.

REFI_001,TYPE_070
REFI_101,REFI_102

_refine_ls_structure_factor_coef

Must be present and of type char.

REFI_003,TYPE_071
REFI_004,TYPE_072

_refine_ls_R_factor_gt
_refine_ls_R_factor_obs

(old)

Must be present (not powder) and of type numb.

REFI_005,TYPE_073
REFI_006,TYPE_074

_refine_ls_wR_factor_ref
_refine_ls_wR_factor_obs

(old)

Must be present (not powder) and of type numb.

REFI_007,TYPE_075
REFI_008,TYPE_076

_refine_ls_goodness_of_fit_ref
_refine_ls_goodness_of_fit_obs

(old)

Must be present (not powder) and of type numb.

REFI_009,TYPE_077
REFI_010,TYPE_078

_refine_ls_number_reflns
_refine_ls_number_parameters

Must be present (not powder) and of type numb.

REFI_011,TYPE_079
REFI_201,REFI_202

_refine_ls_weighting_scheme

Must be present (not powder) and of type char.

REFI_013,TYPE_080
REFI_113

_refine_ls_weighting_details

Should be present and of type char.

REFI_014,TYPE_081
REFI_114,REFI_115

_refine_ls_hydrogen_treatment

Must be present if hydrogen present and of type numb.

REFI_015,TYPE_082
REFI_016,TYPE_083

_refine_ls_shift/su_max
_refine_ls_shift/esd_max

(old)

Must be present (not powder) and of type numb.

REFI_017,TYPE_084
REFI_018,TYPE_085
REFI_118

_refine_diff_density_max
_refine_diff_density_min

Must be present (not powder) and of type numb.

REFI_019,TYPE_086
REFI_020

_refine_ls_extinction_method
_refine_ls_extinction_coef

If one is present, so must the other.

REFI_021,TYPE_088

_refine_ls_abs_structure_details
_refine_ls_abs_structure_Flack
_refine_ls_abs_structure_Rogers

If details present then Flack or Rogers
must be present. If Flack/Rogers then
details must be present.

REFI_023,REFI_024

_refine_diff_density_max
_refine_diff_density_min

Powder papers should have these present.

POWD_001

_refine_ls_goodness_of_fit_all
_pd_proc_ls_prof_wR_factor

At least one of these should be present for a powder paper.

POWD_002

_refine_ls_goodness_of_fit_all

Should be present for a powder paper.

POWD_003

_pd_proc_ls_prof_wR_factor

Should be present for a powder paper.

POWD_004

_refine_ls_R_factor_all
_refine_ls_R_Fsqd_factor
_refine_ls_R_I_factor

At least one of these should always be present for a powder paper.

ATOM_002,TYPE_100

_atom_site_label

Should always be present and of type char.

ATOM_003,TYPE_101
ATOM_004,TYPE_102
ATOM_005,TYPE_103

_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z

Should always be present and of type numb.

ATOM_006,TYPE_104

_atom_site_U_iso_or_equiv

Should always be present and of type char.

ATOM_007,TYPE_105

_atom_site_aniso_label

Should always be present (not powder) and of type char.

ATOM_008,TYPE_106
ATOM_009,TYPE_107
ATOM_010,TYPE_108
ATOM_011,TYPE_109
ATOM_012,TYPE_110
ATOM_013,TYPE_111

_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23

Should always be present and of type numb.

GEOM_001,TYPE_112
GEOM_002,TYPE_113

_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2

Should always be present and of type char.

GEOM_003,TYPE_114

_geom_bond_distance

Should always be present and of type numb.

GEOM_005,TYPE_116
GEOM_006,TYPE_117
GEOM_007,TYPE_118

_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3

Should always be present and of type char.

GEOM_008,TYPE_119

_geom_angle

Should always be present and of type numb.

     

 

 

 


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