4.66. STARTX: Create initial archive file

Authors: Jim Stewart, Jim Holden, Ruth Doherty, George Davenport, Syd Hall and Howard Flack

Contact: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia

STARTX creates or updates an Archive (bdf) with all of the cell, symmetry, crystal and structure information that is known prior to the solution of the structure, exclusive of reflection data. Reflection data is added by subsequent calculations.

STARTX starts, or updates (in upd mode) the Archive by storing the initial information about the file history, any text descriptive of the nature of the structure, unit cell parameters, the unit cell symmetry, the types and number of atoms contained in the unit cell, and various experimental data. The bdf is in essence a repository for known information about the structure under study, and will be available to all subsequent calculations. Other calculations will read this file and add, supersede or delete information as requested.

4.66.1. Unit Cell Data

Cell information is supplied by the cell and cellsd input lines. This information is stored in the lrcell: (the macro name that identifies the logical record containing cell data) record of the bdf, along with the calculated reciprocal cell dimensions and transformation matrices used to transform to orthogonal coordinates (see the Archive at the back of the manual for details).

4.66.2. Symmetry Data

STARTX provides several approaches to entering symmetry information. The most concise way is to use the explicit-origin space group notation (Hall, 1981) with the sgname line. This notation is listed in the supplied symmap file. Space group symmetry can also be defined by entering a latice and/or symtry or spaceg lines. For example the space group A2/a (15:c1 z-unique) may be entered as follows:

sgname        -a_2a


spaceg   a_1_1_2/a 


latice            c     a              
symtry          x,y,z
symtry          1/2-x,-y,z


symtry            x,     y, z  
symtry           -x,    -y,-z
symtry  1/2-x,    -y, z        
symtry       1/2+x,     y,-z       
symtry     -x, 1/2-y, z
symtry      x, 1/2+y,-z
symtry        1/2+x, 1/2+y,-z 
symtry        1/2-x, 1/2-y, z

The number of molecules per cell is entered with the celmol line. The default value is one molecule per asymmetric cell unit. If this is not correct for your structure, use a celmol line - as this greatly assists routines such as PEKPIK, MODEL and PIG.

The contents of the crystal unit cell is with celcon input lines and using internal data (such as the dispersion values) stored for each atom type. A celcon line must be entered for each atom species expected in the structure. The number of atoms of this type expected in the unit cell should also be entered. If the scattering factor name entered is the 'standard' element name, then other atom data such as the atomic weight, the atomic number, the number of electrons, the usual atomic bond radius, the usual Van der Waals radius, and anomalous dispersion scattering terms will be supplied by STARTX automatically. NOTE that if the neutron scattering length is entered all subsequent calculations will assume that neutron data is being processed.

STARTX reads tables stored in the file atomtype.cif for the automatic generation of atomic scattering factors. The use of these tables is dependent upon the value of the atomic number and the number of electrons derived from the scattering factor name or specified explicitly in the celcon input lines. For example, a Cu+ atom could be defined as either Cu+ (or CU+ or cu+ or Cu1+ -- the scattering factor symbol is not case sensitive whereas the atom label which incorporates this symbol is), or CU with fields 3 and 4 set at 29 and 28, respectively.

STARTX also reads atomtype.cif for data to enable scattering factors to be automatically generated for Xrays, electrons and neutrons. Automatic generation is overridden by data entered on formgn, formfx and celcon lines. Scattering factors may be generated for s values out to 6.0 using the method of Fox et al. (1989) A.C. A45, 786. The Stewart, Davidson & Simpson H curve is now generated from the Int Tab Vol 4 coefficients in Table 2.2B, as do all scattering factors. Neutron scattering lengths come from Int Tab Vol 4 Table 2.6. Scattering factors may be printed by entering the line reset psta 4

In a departure from rationality STARTX will permit dummy atom types entered with an atomic number of 0 and a voidflg: or 0 molar weight to be treated as valid types. Use this feature to shoot yourself in the foot in some later calculation like CRYLSQ or FC.

The nature of the radiation may be specified on the STARTX line. Here are the input options:

Radiation typexraysgenerate xray scattering factors
 neutrons generate neutron scattering lengths
 electronsgenerate electron scattering factors
Scatt factor limitssmax smax s value of generated sf <2.0>
 sinc tincr s used for generated sf<0.02>

A scattering factor symbol (also referred to as the atom type symbol) consists of a string of up to eight characters. If the user enters the usual international chemical symbols on the celcon line, these will be used to generate appropriate scattering factor data without the need to enter the atomic number or number of electrons (see last section also).

4.66.3. File Assignments

4.66.4. Examples

STARTX            :the P6122 test in simplest form       
CELL 8.53 8.53 20.37 90 90 120       sgname P 61
2 (0 0 -1)       
CELCON s 6       
CELCON o 6       
CELCON c 12       

STARTX       CELL 11 11 11 90 90 90       
sgname I -4bd 2ab 3
CELCON s 48       
CELCON o 36       
CELCON c 16       
exper 1 1.5418 *9 1.234       
maxhkl 12 8 4 .001  .9       

label  p6122 test 21 june 1982       
CELL 8.53 8.53 20.37 90 90 120
cellsd .01 .01 .01 .01 .01 .01       
latice n p            :alternative is sgname p 61 2 (0 0 -1)
symtry x,y,z       
symtry -x,-y,1/2+z       
symtry y,x,1/3-z       
symtry -y,-x,5/6-z
symtry -y,x-y,1/3+z       
symtry y,y-x,5/6+z       
symtry -x,y-x,2/3-z       
symtry x,x-y,1/6-z
symtry y-x,-x,2/3+z       
symtry x-y,x,1/6+z       
symtry x-y,-y,-z       
symtry y-x,y,1/2-z
CELCON s 6 *8 .350 .869       
CELCON o 6        

4.66.5. References