=========== CRYSTAL STRUCTURE OF CUBI2O4 (space group#79) ======= !=====>THIS IS AN EXAMPLE FILE FOR ORTEP TUTORIAL !==>crystal structure reference: Zeitschrift fur Anorganische !==>und allgemeine Chemie. Bd. 426, (1976) p.1- !==>this is a comment line. All comment lines refer to !===>the previous line of data unless otherwise indicated !==>lines beginning with a ! cannot be present in the !=====>file while running ortep !************************************************** !*****structure info input section***************** !************************************************** 8.4840 8.4840 5.8130 90 90 90 !=====>lattice parameters: a, b, c, alpha, beta, gamma !>the following lines contain the symmetry cards for !>the space group of the structure !>each line contains one of the general atomic positions !>given in the international tables of xray crystallography 0 1 0 0 0 0 1 0 0 0 0 1 0 !==>the zero in column 2 indicates this is a new instruction line !==>the following three groups of four is each a position coordinate !==>in each group the first digit is the coefficient of x, the !===>second digit is the coefficient of y, and the third is the !===>coefficient of z. the fourth is a translation of the coordinate !==>this particular position coordinate is x, y, z. !==>1 0 0 0=x, 0 1 0 0=y, 0 0 1 0=z !==>for a coordinate x+1/2, you use 1 0 0 .5 0 0 -1 0 0 1 0 0 0 0 0 1 0 !==>-y, x, z 0 -1 0 0 0 0 -1 0 0 0 0 1 0 !==>-x, -y, z 2 0 1 0 0 -1 0 0 0 0 0 1 0 !==>y, -x, z !==>for the last symmetry card the column 2 indicator must be non-zero !==>indicator=1 means the end of symmetry information !==>indicator=2 means that the space group contains a lattice !===>translation operation which will be specified on the next line !==>if there is a center of symmetry for the space group then !===>the indicator should be negative !==>in this case there is no center of symmetry so the !==>indicator is positive and there is a lattice translation card !==> to follow 0.5 0.5 0.5 !==>this is the lattice translation card for a !==>+1/2, +1/2, +1/2 translation !>the following lines give the atom positions and characteristics !>each atom position card requires two lines of information, the first !>line contains the position info and the second the thermal parameters 0, 0, 0.5, 0.5, 0.5, 0, CELL CENTER !==>the first zero is an indicator that this is a new line of info !==>the second zero is unnecessary and may be left blank !==>the next three numbers are the position coordinates !==>the third zero indicates that the position coordinates !===>are given in fractions of the unit cell dimensions !==>this zero can also be left blank and be assumed to be zero !==>if a value of 1 is used the position values are read as angstroms !==>the final entry is a label for this atom. the 0,0,0 site is a !===>dummy atom used as a reference point for constructing the cell !==>each atom is numbered sequentially so this is atom #1 0, 0.1,,,,,, 6 !==>again the first zero is an indicator and can be left blank !==>the last digit indicates what type of thermal data is entered !==>if a 4 or 5 is used then anisothermal parameters B11, B22, B33, !===>B12, B13, and B23 are placed in the six center positions !==>a 6 in the last position indicates that spheres are to be drawn of !===>the radius given in the second position (0.1 here) in angstroms !==>the other values are left blank if anisothermal parameters !===>are not used ,, 0.0 0.0 0.0,,CELL CORNER , 0.1,,,,,, 6 !==>Another reference position atom #2 marks the cell corner ,, 0.00000, 0.0, 0.1763,, Cu1 , 0.545, , , , , , 6.0 !==>the first copper atom is atom #3 ,, 0.50000, 0.5, 0.17100,, Cu2 , 0.545, , , , , , 6.0 !==>the second copper atom is atom #4 ,, 0.1683, 0.3316, 0.0,, Bi1 , 0.727, , , , , , 6.0 !==>the bismuth atom is atom #5 ,, 0.0980, 0.2030, 0.6540,, O1 , 1.0, , , , , , 6.0 !==>the first oxygen atom is atom #6 ,, 0.202, 0.101, 0.161,, O2 1 1.0,,,,,, 6 !==>the second oxygen atom is atom #7 !==>here the column 2 indicator is 1 meaning this is the !===>last atom position card !********************************************************* !******instruction section for plotting the structure***** !********************************************************* !>in this section commands are given to perform the plotting !>each line starts with a column 2 indicator which tells the !>program what type of info is to follow on the line: !>0=>a new instruction !>1=>continuation of present instruction !>2=>vector search command !>3=>alphanumeric information !>the next number on the line is a 3 digit command code 3 201 =====> INITIALIZE THE PLOTTER. 3 301 10 8 10 2 =====> SET GRAPH SIZE, VIEWING DISTANCE, AND THE INSIDE MARGIN. !==>plot dimension command:x length, y length, viewing distance !===>and inside margin (values in inches) 3 303 0.0 =====> SET RETRACING FEATURE. !==>retracing command: displacement in inches for retracing !==>this can be used to enhance the perspective of the drawing !==>but takes more plotting time. !==> this option is turned off with a value of zero 3 410 =====> CLEAR THE ATOMS ARRAY. 3 404 155501 1 2 7 0.5 0.5 0.5 =====> TRICLINIC BOX OF ENCLOSURE ABOUT DUMMY ATOM 1 !==>this command defines the region of the crystal structure !==>that is to be plotted !==>155501 is an atom designator code (ADC) !===>the first digit refers to atom #1 !===>the next three digits refer a reference system with !===>its center at 555, and the final two digits refer to !===>symmetry card (operation) #01 !==>this symmetry operation is the identity operator and so !===>it will apply to all atoms in the structure !==>the next three entries are also ADC's but their last !===>five digits are the same as the first ADC (55501) so !===>they are left blank. !==>the first two ADC's indicate a string of atoms to be !==>used as the center of the region to be illustrated. !==>this atom string is called an atom designator run (ADR) !==>in this case 155501 1 indicates that the illustration will !===>be centered at atom #1 which we defined as the cell center !==>the next two ADC's (also known as an atom number run or ANR !===>instead of an ADR since only the atom numbers are used) !===>indicate a string of atoms to be included in the illustration. !===>in this case atoms 3-7 (the copper, bismuth, and oxygen atoms) !===>will be included in the illustration. !==>the last three entries on this line are the fractional !===>lengths of the unit cell parameters to be used as the !===>distances in the three cell dimension directions on either !===>side of the center point to be included in the illustration !==>in this case we include only the contents of the unit cell !===>by limiting the illustration to half a unit cell length !===>in each of the three directions on both sides of the cell center 3 501 155501 255501 265501 255501 255601,, 1 =====> SET THE REFERENCE COORDINATE SYSTEM ( PROJECTION FROM B-AXIS ). !==>this command assigns the coordinate system to the plane of !===>the illustration. !==>155501 designates the origin as before and the following !===>two pair of ADC's are used to form vectors to be assigned !===>as the x and y axis respectfully of the illustration. !==>each pair of ADC's is an vector designator code (VDC) which draws !===>a vector from the first designated atom to the next. !==>the x axis is defined by the VDC 255501 265501 !==>here the first digit of each refers to atom #2 which we !===>defined as the corner of the cell. The vector goes from the !===>position 555 to 655, incrementing in the a axis direction. !==>each increment is equal to the length of the unit cell in that !===>direction !==>thus the a axis of the unit cell is defined as the x axis !===>of the illustration. Similarly the VDC 255501 255601 !===>designates the c axis of the unit cell as the y axis of !===>the illustration 3 502 1 0 2 0 3 0 =====> SET THE REFERENCE SYSTEM ROTATION. !==>this command allows you to rotate the illustration if you !===>wish to. !==>1 refers to the x axis of the illustration and the number !===>following it is the angle of the rotation about this axis !==>2 refers to the y axis of the illustration and the number !===>following it is the angle of the rotation about this axis !==>3 refers to the z axis of the illustration and the number !===>following it is the angle of the rotation about this axis !==>the rotations are performed sequentially x, y, and then z. !==>so if you rotate x first the z axis is no longer perpendicular !===>to the plane of the illustration when the rotation about !===>the z axis takes place 3 604,,,, 3 =====> AUTO SCALE AND POSITION TO ?% PROBABILITY ELLIPSOIDS. 1 511 0.03 !==>this command sequence calculates where the cell edges and !===>atoms and bond will be and notes the overlap so that it !===>can be removed before plotting the illustration. 1, , 255501 255601 255501 265501 255501 256501 1, , 266601 256601 266601 266501 266601 265601 1, , 266501 256501 266501 265501 265501 265601 2, , 265601 255601 255601 256601 256601 256501 !==>these are explicit vector designator codes, VDC's, to calculate !===>the positions of the cell edges 2, , , , , 2, , , 0.01 !==>this line designates the type of bond to use as type 2 !===>with bond radius .01 angstoms 3 3 5 6 7 2 0.5 3.25 0.02 =====> VECTOR SEARCH CODE FOR DRAWING BONDS, PREPARED TO REMOVE OVERLAP. !==>vector search code to calculate positions of the bonds from !===>atoms in ANR 3-5 (Cu and Bi atoms) to atoms in ANR 6-7 !===>(O atoms). thus bonds are to be drawn between coppers and oxygens !===>and between bismuths and oxygens. !==>bonds are of type 2, limited to length between 0.5 and !===>3.25 angstroms with bond radius of 0.02 angstroms. !********************************************************** !*******Plotting Command Section*************************** !********************************************************** 3 999 1 =====> PEN NUMBER FOR DRAWING CELL EDGES !==>this command identifies the pen number for the following !===>to be pen #1 1 811, 255501 255601 255501 265501 255501 256501 1, , 266601 256601 266601 266501 266601 265601 1, , 266501 256501 266501 265501 265501 265601 2, , 265601 255601 255601 256601 256601 256501 3, , , , , 2, , , 0.01 =====> VECTOR DESIGNATE CODES FOR DRAWING CELL EDGES !==>explicit VDC's for drawing the cell edges followed by !===>the designation of the line type and radius in angstroms 3 999 4 =====> PEN NUMBER FOR DRAWING COPPER ATOMS !==>this command identifies the pen number for the following !===>to be pen #4 1 701 ,,,, 3 4 !==>this command plots atoms in ANR 3-4 (copper atoms) 3 999 3 =====> PEN NUMBER FOR DRAWING BISMUTH ATOMS !==>this command identifies the pen number for the following !===>to be pen #3 1 701 ,,,, 5 5 !==>this command plots atoms in ANR 5-5 (bismuth atoms) 3 999 2 =====> PEN NUMBER FOR DRAWING OXYGEN ATOMS !==>this command identifies the pen number for the following !===>to be pen #2 1 701 ,,,, 6 7 !==>this command plots atoms in ANR 6-7 (oxygen atoms) 3 999 1 =====> PEN NUMBER FOR DRAWING BONDS !==>this command identifies the pen number for the following !===>to be pen #1 2 812 3 3 5 6 7 2 0.5 2.25 0.02 =====> VECTOR SEARCH CODE, DRAW BONDS BETWEEN ANIONS AND CATIONS. !==>this command plots the bonds. !==>the codes are the same as the search above to !===>remove overlap , -1 !==>this code marks the end of the file