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 R_all = <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 F_A 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.