The platon crystallographic package - səhifə 48
major disorder components and those less than 0.5 as minor disorder components. The usual
transformations on input coordinates are restricted. In general it will be necessary to supply
disordered molecules as connected sets. The calculation of distances and angles etc. will
extend only to entities involving the major disorder component or the minor disorder
component but not between them.
2.4.3 – Molecules, Residues and ARU's
The concepts of molecules and residues are related but not always synonymous with those
in the PLATON context. A residue is defined as a part of the structure that is connected by
intra-molecular bonds only and is associated with a number (residue number). A structure
may thus contain one or more residues (molecules, ions, chains or network). Residues may
be chemically equivalent or chemically distinct. An
ARUis defined as the unique
asymmetric part of a residue connected by intra-molecular bonds only. One or more
may join by crystallographic symmetry into one residue. A particular
ARUis designated by
a code: [nijk.rr] where
ndenotes the symmetry operation with respect to the basic molecule,
ijkthe translation with respect to 555 and
rrthe residue number. The crystal structure of
sucrose (space group P2
) thus consists of two molecules (e.g. [1555.01] and [2545.01]) but
only one residue.
2.4.4 - Population parameters
A distinction should be made between 'population parameters' as used in SHELXL
sof) and those in the CIF (indicated here with
PP) and in PLATON. Most
refinement packages refine a population parameter that is defined as
sof = PP / ssn, where
ssnis the site symmetry number. E.g. A full weight atom on an inversion center has in
PP=1.0 when fully occupied but
sof= 0.5 in SHELXL since
2.5 – Instruction Summary
This section provides a description of the available instructions for keyboard input. The
more common ones are also available through mouse-clicks on menu-items. The
instructions are grouped together as compound specific, calculation, plot, list and general
instructions. The logical order of the geometry calculations is intra-molecular, inter-
molecular and coordination. In the description of individual instructions below the
- (Sub)keywords are in uppercase and user data in lower case
- Data in parentheses are optional.
- Data in  are defaults.
- Choices are separated by a slash.
Note: parentheses in atom names (on input) are ignored except for that Ag denotes the atom
type and Ag() the individual atom. Lower case input is automatically converted to upper
case. Instruction records with a blank character in position 1 or a # are ignored. Instruction
records may be continued with data on the next line by placing the symbol = at the end of
2.5.1 - Directives Preceding all Calculations
The instructions given in this section will be necessary only in special situations.
188.8.131.52 - ROUND ([ON]/OFF) ()
This instruction defines whether the primary input data and the geometrical parameter
values derived from them will be rounded based on their s.u.'s or not. When rounding is ON,
derived data will be calculated starting from rounded coordinates. By (Acta Cryst.) default,
coordinates and derived data (bonds, angles etc.) are rounded following the 1-19 rule. No
rounding will be done when the ROUND feature is OFF. Rounding can be changed to
follow the 1-9 rule with
ROUND 1or to the 1-29 rule
184.108.40.206 - PARENTHESES ([ON]/OFF)
By default, in listings, the numerical part of an atomic label will be enclosed within
220.127.116.11 - NOMOVE ([ON]/OFF)
Keep atoms at input positions. This feature avoids automatic repositioning to symmetry
related positions in the setup phase of the connectivity tables. The MOMOVE instruction
can be useful when the input data set is already a connected set. Applications include CIF's,
disordered structures and molecules on symmetry positions.
More detailed control is available with the
18.104.22.168 - INCLUDE el1 el2 ...
Only the elements specified in the include list will be included in the calculations.
INCLUDE C N O
22.214.171.124 - EXCLUDE el1 el2 ...
The elements specified in the exclude list will be excluded from all calculations.
126.96.36.199 - DOAC el1 el2 ....
The elements N, O, Cl, S, F and Br are treated as potential donor/acceptor atoms for
hydrogen bonding by the program. This list will be replaced by the one specified in the
DOAC N O
188.8.131.52 - HBOND (NORM) p1 p2 p3
Default criteria for hydrogen bonds are: distance between donor and acceptor atom less than
the sum of their van der Waals radii + p1 ( = 0.5 angstrom); distance H to acceptor atom less
than sum of corresponding van der Waals radii + p2 (= -0.12 angstrom) and angle D-H...A
greater than p3 (= 100 degree). The default values may be changed with the HBOND
instruction before the subsequent calculations. Alternatively, the same data could be
supplied on the
D-H distances will be normalized to standard values when the keyword
Their default settings may be changed with
The current H-bond criteria and normalization values with associated SET PAR numbers
[SET PAR 8 new-value]
[SET PAR 9 new-value]
[SET PAR 10 new-value]
[SET PAR 294 new-value]
[SET PAR 295 new-value]
[SET PAR 296 new-value]
[SET PAR 297 new-value]
[SET PAR 298 new-value]
SET PAR 298 0.97to normalize O-H on 0.97 Angstrom.
184.108.40.206 - LSPL atom_name1 atom_name2 ..
This instruction specifies the set of atoms for which a least-squares plane should be
calculated. In this way it is possible to include special planes in the following calculations
that include the generation of least-squares planes for planar parts in the structure.
LSPL C1 C2 C3 C4
220.127.116.11 - RING atom_name1 atom_name2 ...
Rings in the structure up to 8 membered are found automatically. This instruction provides a
facility to include larger rings (up to 30 membered) in the calculations. The atoms should be
specified in bonded order. This ring will be taken into account is the calculations and tables.
RING O1 O2 O3 O4
18.104.22.168 - LINE atom_name1 atom_name2
Explicit line specification between two not necessary bonded atoms. This line will be
included in the following analysis and tables.
LINE Cu1 Cu2
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