Bijvoet centre for biomolecular research, vakgroep kristal- en structuurchemie, university of utrecht

9.3 PLATON - ANALYSE Menu

 

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SPGR space-group-name

 Space group symbol. See 9.4.7 below for more details.

LATT (P/A/B/C/I/F) (A/C)

First parameter specifies the Bravais lattice type and the second whether the lattice is acentric

or centric.

SYMM symmetry-operation

Symmetry operation. See  9.4.7 below

ATOM atom_name x y z (pop) (sig(x) sig(y) sig(z)) (spop)

This specifies the positional parameters, the population and their estimated standard

deviations. The atom_name should conform some rules in order to be acceptable since it is

interpreted. The first one or two characters should correspond to an element name known to

the program (see Appendix V). The  number of characters of the element type and the

attached digital number cannot  exceed four. ' and " are allowed as part of an atom name.

Labels not conforming with the PLATON-rules are modified in a new label including the

symbol #. The atom-name may contain parentheses enclosing the numerical part.

UIJ  atom_name U11 U22 U33 U23 U13 U12

Anisotropic thermal parameters. Note the order of the components that is the same as in

SHELX but often different in other systems (such as the XRAY and XTAL systems).

TF = exp[-2*pi

2

(U11*h**2(a*)

2

+...+2*U12*h*h*(A*)(B*)+...)]

SUIJ atom_name sig(U11) sig(U22) sig(U33) sig(U23) .. sig(U12)

Estimated standard uncertainties (e.s.d’s)  for the anisotropic thermal parameters.

U     atom_name U sig(U)

Isotropic temperature factor along with its associate standard deviation.

BIJ  atom_name Beta11 Beta22 Beta33 Beta23 Beta13 Beta12

Anisotropic thermal parameters. Note the order of the  components.

TF = exp[-(Beta11*h

2 

+Beta22*k

2

 +...+2*Beta12*h*h+...)]

Definition: Beta11 = 2*pi

2

 *astar

2

            Beta12 = 2*pi

2

*astar*bstar.

     

SBIJ atom_name sig(Beta11) .. sig(Beta23) .. sig(Beta12)

Estimated standard deviations for the anisotropic thermal parameters.

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B    atom_name B sig(B)

Isotropic temperature factor along with its associate standard deviation. Definition: B =

8*pi

2

*U

TRNS -n.klm

Facility to influence the applied symmetry operation for the first atom in a new residue. (see

appendix I)

TRNS  n.klm

When placed in front of an ATOM card this instruction will transform the input coordinates

on that card by the named symmetry operation: n is the number of the symmetry operation

and k,l,m are the translations. (see 4)

TRNS T11 T12 T13 T21 T22 T23 T31 T32 T33 (SH1 SH2 SH3)

Transformation matrix on cell axis and origin shift to be applied to the data following (CELL

parameters, atomic coordinates and thermal parameters).

Example:

TITL NI-COMPOUND

CELL NI .123 .544 -.176 1 .001 .002 .001 0.0

UIJ  NI .011 .013 .025 -.011 .004 .009

SUIJ NI .001 .001 .002 .002 .002 .001

ATOM C1 .345 .675 -.334 1 .010 .009 .005 0.0

U    C1 0.04 0.01

     (etc)

7 Space group symmetry

Space group symmetry is handled in PLATON with a general space group symmetry

management routine that permits the specification of the symmetry either explicitly in terms

of the general equivalent positions as presented in the International Tables or implicitly in

terms of space group generators. The generators for all space groups in their standard setting

and some commonly used non-standard settings are also implicitly retrievable by the program

from internal tables (see tables below) on the basis of the specified name of the space group

(e.g. R-3m)

EXAMPLE: The symmetry for space group nr. 19 (P2

1

2

1

2

1

) may be specified either as:

    

LATT P A

     SYMM X,Y,Z

     SYMM 1/2 + X, 1/2 - Y, -Z

     SYMM -X, 1/2 + Y, 1/2 - Z

     SYMM 1/2 - X, - Y, 1/2 + Z

or

       LATT P A

     SYMM 1/2 + X, 1/2 - Y, -Z

     SYMM -X, 1/2 + Y, 1/2 - Z

or

           SPGR P212121

LATT card should precede any SYMM card in order that the symmetry arrays are initialised

to either, by default, a primitive non-centrosymmetric lattice or to the specified lattice type:

(P/A/B/C/I/F) and (A)Centric type (A/C). The general equivalent positions should be given as

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specified in International Tables and should have the centre of symmetry at the origin, in the

case that the space group is centrosymmetric. The symmetry operation SYMM X,Y,Z is

always implicitly assumed as the first symmetry operation and needs not be given although

any redundancy in the symmetry input will be ignored.

Note: Rhombohedral lattice types (in hexagonal setting) should be specified explicitly using

an extra symmetry generator. Thus the generators for space group R3 are:

           LATT P A

     SYMM -Y, X-Y, Z

     SYMM 1/3+X, 2/3+Y, 2/3+Z

The same space group on rhombohedral axes should be specified as

R3R.

The translation part may be specified either as a ratio or as a real (e.g. 1/4 or 0.25).

Monoclinic-b is taken as the standard setting for monoclinic space groups. Other settings are

to be specified by the full space group name: e.g. P112 for the monoclinic-c setting of P2.

Non-standard orthorhombic settings such as space group  A2aa may be handled by specifying

Ccc2 -cba on the SPGR card (see International Tables Vol A). In fact the program

automatically modifies the input line accordingly for non-standard settings (see table below).

The standard setting symmetry is than transformed accordingly. 

Note: Symmetry may also be presented in the SHELX style. However a LATT card should

always be supplied since the default symmetry of PLATON is always P1 whereas SHELX

defaults to P-1.

The names of the space groups known to the program are given in the following table and are

in accordance with the usage in the CAMBRIDGE CRYSTALLOGRAPHIC DATA BASE

files.

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