Appendix I - Recognized Coordinate Data Input Standards
Parameter data may be supplied to PLATON in various formats. They include:
- CIF - The standard Crystallographic Interchange Format
- RES - SHELX standard (No s.u's !)
- FDAT - The old Cambridge Crystallographic database data Format
- PDB - A rather loose format in use in the modeling and protein world.
- SPF - A rather flexible local format ideal for manual free format input ( Section I.1)
- CART3D - Angstrom Coordinate Format input specification.
Notes:
- A CIF or SPF style file is needed when s.u.'s on the derived geometry parameters are
desired as part or the calculations.
- PLATON works out the parameter file type from its contents and not from the file
extension.
A-I.1 – SPF FILE RECORD TYPES
The SPF parameter file format (modeled on that of the original PLUTO program) is
designed as a flexible free format data entry standard. It allows for easy ad-hoc data entry
for geometry calculations and graphics tools. The SPF-format is card image oriented. The
first four characters on a card specify the nature of the data that follow on that card. Data
that are not needed for the current program are simply skipped. All data are read free
format. All input data are transformed to upper case except for the text on the TITL card. A
card image may be continued on the next one by putting an '=' sign on the one to be
continued. This does not apply for a TITL card. PLATON contains tools to convert those
data to either RES or CIF format.The SPF-file is card image oriented.
A-I.1.1 - TITL text
This text may be used for various titling purposes in the graphics output. It may be
overridden at any time by another TITL instruction.
A-I.1.2 - CELL (wavelength) a b c alpha beta gamma
Optional wavelength and cell parameters in Angstroms and degrees respectively. No CELL
card is needed for Angstrom data input. The wavelength is used for the calculation of the
linear absorption coefficient.
A-I.1.3 - CESD sig(a) sig(b) sig(c) sig(alpha) sig(beta) sig(gamma)
This optional card specifies standard deviations in the cell parameters. No CESD card is
needed for Angstrom data. The cell e.s.d. is combined with the coordinate e.s.d. for the
calculation of the e.s.d. in derived parameters.
A-I.1.4 - SPGR space-group-name
Space group H-M symbol. See Appendix-III for more details. Space group P1 is assumed
when no symmetry is specified. The symbol may contain spaces.
Example: SPGR P21/c or SPGR P 21/c
A-I.1.5 – HALL Hall-Symbol
Alternative specification of the space group (Hall, 1981).
Example: HALL -P 2ybc
A-I.1.6 - 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. This card is needed only when no SPGR is specified
Example: LATT A C
A-I.1.7 - SYMM symmetry-operation
SYMM cards are needed only when no SPGR is specified
Example: SYMM -x, ½ + y, ½ - z
A-I.1.8 - 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
uncertainties. 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. The atom-name may contain parentheses
enclosing the numerical part. Parentheses do not count. The characters ' 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' part can optionally be omitted since every card
that does not start with a known keyword is tested to be an ATOM record. The minimum
number of numerical items is three, the maximum eight.
Acceptable labels are: Ag, Zn(2), C(2A), Fe1b
Note: QW is equivalent to O and Q1 is equivalent to C1.
A-I.1.9 - 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*K*(A*)(B*)+...)]
A-I.1.10 - SUIJ atom_name sig(U11) sig(U22) sig(U33) sig(U23) .. sig(U12)
Estimated standard deviations for the anisotropic thermal parameters.
A-I.1.11 - U atom_name U sig(U)
Isotropic temperature factor along with its associate standard deviation.
A-I.1.12 - 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*K+...)]
Definition: Beta11 = 2*pi**2*astar**2
Beta12 = 2*pi**2*astar*bstar.
A-I.1.13 - SBIJ atom_name sig(Beta11) .. sig(Beta23) .. sig(Beta12)
Standard uncertainties for the anisotropic displacement parameters.
A-I.1.14 - B atom_name B sig(B)
Isotropic temperature factor along with its associate standard deviation.
Definition: B = 8*pi**2*U
A-I.1.15 - TRNS -n.klm
Facility to influence the applied symmetry operation on the first atom in a new residue in
the process of setting up a connected coordinate set.
A-I.1.16 - 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.
A-I.1.17 - TRNS T11 T12 T13 T21 T22 T23 T31 T32 T33 (SH1 SH2 SH3)
This optional instruction may be used to transform the data to a new unit cell. The first nine
data items are the elements of the matrix that describes the transformation of the cell axes
( = new axis in terms of old ones). The origin may be shifted over the vector (sh1,sh2,sh3).
Related matrices are used to transform the atomic coordinates. The TRNS instruction should
be given before any ATOM card is read and before the CELL card when it is to be
transformed as well.
A-I.2 - ANGSTROM DATA FORMAT
Files with just positional parameters, but not preceded by CELL and symmetry cards are
understood to be Angstrom data in a Cartesian system. The coordinate data may be preceded
by an ANGSTROM card with optionally a multiplication factor to transform the data to
angstrom units. This can be convenient when data originate from quantum chemistry
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