PLATON - MANUAL
1.0 - INTRODUCTION TO PLATON
PLATON brings together, in the context of a single program, a large
variety of tools to be used in the process of a single crystal
structure determination. This manual only discusses the available tools
for the calculation and analysis of the geometrical results. Other
implemented tools are documented elsewhere.
PLATON may be used in conjunction with and complements structure
determination programs such as SHELXS-97 and refinement programs such
as SHELXL-97. The build-in PLUTON link may be used with the same data
files for more elaborate graphics such as molecule packing plots.
PLATON is designed for the automated generation of a variety of
geometrical entities such as bond distances, bond angles, torsion
angles, least-squares planes and ring-puckering parameters. All derived
parameters are accompanied by standard deviations that are calculated
by numerical methods from the supplied standard deviations in the
primary input parameters.
The free format input data generally consist of two types of data that
are in general but not necessarily supplied separately to the program.
The crystallographic or molecular data such as coordinates, thermal
parameters, cell dimensions and symmetry, possibly generated by the
structure determination or refinement program, may be read from a file.
Instructions are conveniently entered directly from the keyboard or
from menus.
In general only global instructions are necessary to obtain tables of
the required derived molecular geometry data. Specific information such
as atomic radii and other properties related with the element types
involved are by default drawn from internal tables. The simple
instruction CALC will automatically execute virtually all calculations
that may be of interest for the supplied parameter set.
The set of available analysis procedures includes those for rigid-body
thermal motion with bond distance correction, puckering analysis
(including the Cremer & Pople variety), hydrogen bonds (including
an analysis in terms of networks), voids in the structure and
five-coordination (Berry pseudorotation). Appropriate references to the
literature are given in the output listing.
The calculations are complemented with graphics facilities such as
anisotropic displacement ellipsoid plots, Newman projection plots and
projection plots of the structure on the various least-squares and ring
planes.
PLATON is written in FORTRAN-77 (with a small graphics driver written
in C to interface to X-Windows and easily implemented on UNIX systems
(Silicon Graphics, DEC, Linux etc.). PC-Windows and VMS versions are
also available.
Note: PLATON turns out to be never finished. There are always new
horizons. It is constantly improved with new facilities as their need
arises in the course of the large variety of structure determinations
that are carried out in our laboratory. In view of the extremely large
number of options of the program, combined with the unique
characteristics of each new crystal structure examined with the
program, problems may arise in non-standard cases. The author will be
interested in any user comment and suggestions for extentions for
future releases.
1.1 - Manuals for PLATON Options & Links not discussed here
2.0 - INTRODUCTORY EXAMPLE
The following example, assumed to run on a UNIX system ,of the
structure of SUCROSE (neutron data) should provide an introduction to
the use of this program and its potential.
The structural parameters are assumed to reside on a disk file named sucrose.spf
for which the free format contents are listed in part below:
TITL SUCROSE (ACTA CRYST. (1973),B29,790-797)
CELL 1.5418 10.8633 8.7050 7.7585 90 102.945 90
CESD 0.0005 0.0004 0.0004 0 0.006 0
SPGR P21
ATOM C1 0.29961 0.35792 0.48487 0.00008 0.00000 0.00012
BIJ C1 0.00274 .00376 .00584 .00004 .00094 .00006
SBIJ C1 .00006 .00009 .00012 .00009 .00007 .00006
ATOM C2 0.31253 0.47474 0.63600 0.00009 0.00015 0.00012
BIJ C2 .00304 .00498 .00641 -.00063 .00073 -.00043
SBIJ C2 .00006 .00010 .00013 .00009 .00007 .00007
ATOM C3 0.28545 0.63673 0.56447 0.00009 0.00015 0.00013
BIJ C3 .00321 .00437 .00965 -.00071 .00196 -.00017
SBIJ C3 .00007 .00010 .00015 .00010 .00008 .00007
ATOM C4 0.37404 0.67095 0.44198 0.00010 0.00015 0.00014
BIJ C4 .00400 .00403 .01003 .00006 .00243 -.00021
SBIJ C4 .00007 .00010 .00015 .00011 .00009 .00007
etc. etc.
ATOM H601 .34766 .27804 .16026 .00029 .00037 .00035
BIJ H601 .00909 .01261 .01234 -.00197 .00287 -.00210
SBIJ H601 .00026 .00039 .00040 .00032 .00027 .00026
A PLATON calculation may be invoked for this data set with the command platon
sucrose. As a result the data set sucrose.spf is loaded and,
since this file does not contain an END instruction at the end of the
file, the program comes, after that the end-of- file has been reached,
with the prompt >> to receive more data and/or instructions. A
calculation of the intra-molecular geometry may now be invoked with the
instruction CALC INTRA. The results are written to a disk file (in this
case sucrose.lis). An analysis of short inter-molecular contacts
is performed with a subsequent CALC INTER instruction. The analysis may
be completed with a CALC COORDN instruction that gives a listing of all
bonds and angles about all atoms (excluding C and H) involving atoms
within a 3.2 Angstrom coordination sphere.
An anisotropic displacement ellipsoid plot (commonly called ORTEP) is
obtained with PLOT ADP. The plot may be rotated over 45 degrees about
the vertical Y-axis with the instruction VIEW YROT 45. The session may
be closed with the instruction END.
3.0 - ON HOW IT WORKS
This section on the program internals should provide a framework to
understand the effects of the various available instructions.
The input atomic coordinates (x, y, z) are with reference to
user-defined axes (a, b, c), which will usually be either
crystallographic unit cell axes or an arbitrary orthogonal set; these
coordinates are input as fractions of the unit cell edges or as
Angstrom units (in the latter case they are converted and stored as
fractions of dummy cell edges). A second, orthogonal system (A, B, C)
with coordinates (XO, YO, ZO) in Angstrom units is set up internally
(see J.D. Dunitz, X-Ray analysis and structure of Organic molecules,
p236): A is a unit vector along a, B is a unit vector normal to a in
the ab-plane, and C is normal to A and B. B will coincide with b in
monoclinic cells in the b-setting. If the input axes are orthogonal,
the two sets of axes a,b,c and A,B,C are coincident. The third system
is the plotting coordinate system in cm: XP across the picture from
left to right, YP up the picture from bottom to top and ZP out of the
paper. All these axial sets are right-handed and absolute configuration
is preserved in all rotations.
As atoms are input to the program, they are stored in the x,y,z and
XO,YO,ZO axes systems. Each atom also has additional information stored
for it such as estimated standard deviations, thermal motion
parameters, a name (the embedded element name is used by default to set
various radii to be used during the subsequent calculations) and
various bit flags such as the inclusion bit. Coordinate data are
checked for duplications on input and, if so, rejected. The atom list
is sorted on the basis of the implicit information on atom type in the
label (unless overruled). Atom labels not conforming to the required
format are renamed with a # added..
A CALC instruction generally initiates a distance search on the basis
of internal or usersupplied covalent radii. In the INTRA mode this
results in the setup of an array that stores per atom all connections
that are found. This list is used subsequently by a geometry listing
routine that generates all unique bond distances, bond angles and
torsion angles. Simultaneously with the setup of the connectivity array
all atoms are transformed (when necessary, unless overruled) to obtain
a connected set. In addition, in the case that the molecule lies on a
special position, the primary coordinate list is expanded with
additional symmetry generated atoms in order to handle the geometry of
the complete molecule.
3.1 - Cell Transformation
PLATON can be used to transform CELL, SYMM and Coordinate data
according to a specified transformation matrix.
The general format of the transformation instruction line is:
TRMX r11 r12 r13 r21 r22 r23 r31 r32 r33 t1 t2 t3
in which 'r11 r12 r13' expresses the new a-axis in terms of the old
[ e.g. a' = b + c is encoded as 0 1 1
t1 t2 t3 indicate a shift of origin after the cell transformation.
The TRMX will affect only data following it !
Symmetry operations may be protected for transformation by placing []
e.g. SPGR [C2/C]. This may be useful when the target space group is
known and the transformation doesn't seem to work otherwise (which
should of course never happen ...
The transformed data may be written out as a .res by
1 - click on proper button in the PLATON opening window
or:
2 - CALC SHELX
4.0 - TERMS AND NOTIONS
Atomic coordinates as input will be transformed in
general by symmetry operations following certain rules. In the default
automatic mode this will result in a connected set with residues
properly positioned within the unit cell range. The symmetry operation
applied to the input data will be listed under the header trans in the
atomic coordinates listing and is encoded as n.ijk. n stands for the
number of the symmetry operation as specified on the first page of the
output listing and ijk for the unit cell translations in the three
directions relative to 555: ijk=564 means 1 positive translation in the
b direction, 1 negative translation in the c direction and none in the
a direction.
The automatic mode transformation may be overruled for a
given atom by preceding the data for that particular atom by a TRNS
instruction e.g. TRNS 3.564. This facility may be used to determine
the part of the molecule that is to be considered as the asymmetric
part of a symmetrical molecule.
The transformation to be applied only to the first atom
as a starting point of a new residue can be forced with a negative
symmetry transformation code e.g. TRNS -5.354. Its position in the
input stream determines the atoms to which it will apply. The input
stream may contain several of such instructions, each apply to the
atoms that follow until overruled by a new one. Their effect will only
be on atoms that are choosen to start a new residue.
See also NoMove
The program attempts to manage the problems that are
encountered with several types of disorder. Only two-fold disorder is
allowed. Populations higher than 0.5 are understood as 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 both.
The concepts of molecules and residues are related but
not always synomymous within the PLATON realm. A residue is defined as
a part of the structure that is connected by intra-molecular bonds only
and is associated with a number. A structure may thus contain one or
more residues. Residues may be chemically equivalent or chemically
distinct. A molecule is defined as an asymmetric part of the structure
connected by intra-molecular bonds only. Several molecules may join by
crystallographic symmetry into one residue. A particular molecule is
designated by a code: [nijk.rr] where n denotes the symmetry operation
with respect to the basic molecule, ijk the translation with respect to
555 and rr the residue number. The structure of sucrose thus consists
of two molecules (e.g. [1555.01] and [2545.01]) but only one residue.
A distinction should be made between 'population
parameters' as used in SHELXL (indicated with 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 ssn is the site symmetry number.
e.g A full weight atom on an inversion center has in
general PP=1.0 when fully occupied but sof = 0.5 in
SHELXL since ssn = 2.
This Chapter provides a description of the available
instructions available for Keyboard input. The more common ones are
also available through mouse-clicks on menu-items. They are grouped
together as compound specific, calculation, plot, list and general
instructions.
The logical order of calculations is intra-molecular,
inter- molecular and coordination geometry.
In the description of individual instructions below the
following applies: - (Sub)keywords are in uppercase and user data in
lower case - Data in parentheses are optional. - 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. Lines with a
blank character in position 1 are ignored. Input lines may be continued
with data on the next line by placing the symbol = at the end of the
line.
The instructions given in this section will be necessary
only in special situations.
ROUND (ON/OFF) (range)
This option defines whether primary input data and
derived geometrical parameter values will be rounded based on their
standard deviations or not. When rounding is on, derived data will be
calculated starting from rounded coordinates.
By 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 the 1-9 rule with: ROUND
1
or to 1-29 rule : ROUND 3
Example: ROUND OFF
PARENTHESES (ON/OFF)
By default, the numerical part of an atomic label
will be enclosed within parentheses.
Example: PARENTHESES OFF
NOMOVE ([ON]/OFF)
Keep atoms at input positions. This feature avoids
automatic repositioning to symmetry related positions in the setup
phase of connectivity tables.
MOMOVE 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 TRNS
instructions.
Example: NOMOVE OFF
INCLUDE El1 El2 ...
Only the elements specified in the include list will
be included in the calculations. ELn may be Met for metal.
Example: INCLUDE C N O
EXCLUDE El1 El2 ...
The elements in the exclude list will be excluded from
all calculations.ELn may be Met for metal.
Example: EXCLUDE H
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 instruction.
Example: DOAC N O
HBOND 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.
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.
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.
LINE atom_name1 atom_name2
Explicit line specification between two not
necessarely bonded atoms.
FIT atom_name1 atom_name2 ....
Pairwise Molecule FITTING. PLATON contains a FIT
routine based on quaternion rotation (A.L. Mackay, Acta Cryst. (1984),
A40, 165-166).
The general instruction to fit two molecules or
residues is:
FIT At11 At21 At12 At22 .....(etc)
where atoms to be fitted are given pairwise.
Note: The FIT instruction may be broken up over more
than one line. Lines that are to be continued should end with '='.
There are two modes of operation:
-
when specified before any CALC instruction, the
actual calculation will be done along with the subsequent CALC GEOM or
CALC INTRA calculation. Listing of the results will be on the '.lis'
file only.
-
when specified after a CALC INTRA or CALC GEOM
calculations will be done directly. Listing of the results of the
calculation are both on the interactive output window and in the
listing file.
A special case is the situation where the two
molecules to be fitted have similar numbering of the atoms. The
automatic sorting feature of PLATON will put the atoms in the same
order. In such a case, specification of only one atom from each of the
molecules will be sufficient to fit all non-hydrogen atoms in both
molecules
Example: FIT O11 O21
CALC
The full range of molecular geometry calculations will
be carried out automatically with a the single keyword instruction
CALC. This includes all the calculations that may be executed
alternatively with the instruction sequence CALC INTRA, CALC INTER,
CALC COORDN and CALC METAL.
CALC INTRA ((El1 r1 El2 r2 ..)/(TOLA p1)) (NOBOND)
(NOANG) (NOTOR) (NOLSPL) (NORING) (NOTMA) (NOBPA) (NOSTD) (WLSPL)
(NOPESD) (NOMOVE) (NOSYMM) (TOLP t2)
The default instruction CALC INTRA produces a full
calculation and listing of all relevant intra-molecular geometrical
parameter options using default covalent radii drawn from internal
tables. Atoms with distances less than the sum of their covalent radii
plus a tolerance (TOLA = 0.4 Angstrom) are considered to be bonded. The
default radii values may be modified with their explicit specification
(in which case TOLA is set to zero, unless specified explicitly).
Alternatively the parameter TOLA may be modified. In the automatic
radii mode an additional 0.6 Angstrom is added to the tolerance to
catch (Earth)alkali to non-metal contacts.
The calculation and listing of bonds, bond angles,
torsion angles, least-squares planes, rings, angles between bonds and
least-squares planes and thermal motion analysis may be suppressed with
the specification of the sub-keywords NOBOND, NOANG, NOTOR, NOLSPL,
NORING, NOBPA and/or NOTMA. The calculation of standard deviations may
be suppressed with NOSTD.
The NOMOVE sub-keyword has the effect that atoms are
left at their input positions in the course of the generation of a
connected set.
TOLP is an out-of-plane deviation parameter (by default
0.1 Angstrom) that determines the inclusion of an atom in the process
of automatic least-squares plane search.
NOPESD , when specified, has the effect that the e.s.d.
of the plane parameters is not included in the calculation of the
e.s.d. in out-of-plane deviations. WLSPL invokes mass-weighted
least-squares plane calculations as opposed to unit weighted. NOSYMM
limits the search for connections within the input coordinate set
without the application of translation or rotation symmetry.
Example: CALC INTRA NOLSPL NORING
CALC GEOM (SHELX/OMEGA/MOGLI/EUCLID) (NOMOVE) (EXPAND)
This instruction executes a short intra calculation,
mainly producing a list of bond distances, bond angles and torsion
angles, as an alternative for the exhaustive CALC INTRA calculations.
The sub-keyword SHELX may be used to generate an ordered coordinate
file suitable for SHELX; OMEGA generates a file suitable for the
tabulation of primary and derived parameters; MOGLI results in a
DGE-file suitable for the program MOGLI and EUCLID gives a new SPF
style file.
The NOMOVE sub-keyword has the effect that atoms are
left at their input positions in the course of the generation of a
connected set.
The EXPAND option may be useful for the generation of a
file with the complete molecule as opposed to just the unique part.
Example: CALC GEOM EUCLID EXPAND
CALC TMA
This invokes the execution of a rigid-body thermal motion
analysis and the calculation of derived quantities. It is automatically
included in a CALC INTRA calculation. Note: No TMA analysis is done
when the residue contains too few atoms or when the R-index of the
observed and calculated Uij's is too high.
CALC INTER (El1 p1 El2 p2 ..)/(TOLR p1)
Short inter-molecular contacts are listed with this
instruction. By default van der Waals radii drawn from internal tables
are used in conjunction with a default tolerance (TOLR = 0.2 Angstrom).
Hydrogen bonds are automatically found and analyzed.
CALC HBOND (p1 p2 p3)
This instruction provides a subset of the information
generated with the CALC INTER instruction and may be of use when
interest is concentrated on H-bonds.
CALC COORDN (p1/El1 r1 El2 r2 .. (NOANG) FIVE (TBA))
This instruction provides for the analysis of
coordination spheres. Bond distances and bond angles are calculated for
atoms within the specified sphere. By default such a calculation is
done for all atoms (excluding C and H) and with radius 3.2 Angstrom.
This default may be changed with the specification of the desired
value. Alternatively a list of selected elements and their
corresponding coordination radii may be specified for the coordination
geometry calculations. Bond angles may be excluded from the listings
with the NOANG sub-keyword. A Berry pseudo rotation analysis is carried
out automatically when an atom is found to be bonded to exactly 5
atoms. Such a calculation may be enforced for the five shortest
contacts with the sub-keyword FIVE optionally followed with the value
for the trans-basal-angle (default 150 degree).
CALC COORDN atom_name p1
The coordination geometry about a single atom may be
examined with this instruction.
Example: CALC COORDN O3 3.2
CALC METAL (p1)
Distances between metal atoms less than p1 (default 10
Angstrom) are calculated. This option is included in the default CALC
calculations.
CALC VOID (LIST) (GRID p1) (TOLV p2)
This option may be used to check the structure for voids
as possible sites for solvents. The GRID (default value 0.4 Angstrom)
and the minimum VOID radius (1.2 + p2 Angstrom) may be changed (default
p2 = 0.0). The LIST option gives a map on the lineprinter. Positions
with a shortest contact distance to the van der Waals surface of at
least 1.2 + p2 Angstrom are indicated with >. Solvent accessible
areas are indicated with a dot. Blank areas indicate small voids, all
other gridpoints are within the molecular van der Waals volume. Note:
This option may also be used to study cases where the unit cell
contents are misplaced with respect to the symmetry elements, since
this fault will generally result in both areas with short molecular
contacts and areas with voids. The VOID option is more compute
intensive than the rest of the instructions. It is advised to run this
option in BATCH mode.
CALC DIST (eltype p1)
A distance scan is done for all vectors between the
specified element and within the specified radius. By default a scan is
done for H-atoms.
Example: CALC DIST I 4.0
DIST Atom_name1 Atom_name2
With this option a distance between two specified and
not necessarily bonded atoms may be calculated between atoms in the
atom_array.
ANGL Atom_name1 Atom_name2 Atom_name3
The angle between the specified and not necessarily
bonded atoms is calculated.
TORS Atom_name1 Atom_name2 Atom_name3 Atom_name4
The dihedral angle involving the four specified atoms
(not necessarily bonded) is calculated.
LSPL Atom_name1 Atom_name2 Atom_name3 Atom_name4 ...
The least-squares plane determined by the specified
atoms is calculated.
The program provides graphics options to support the
geometry analysis. A number of options are supported only from the menu
(STEREO, MONO).
PLOT (LSPL/PLAN/RING/RESD) (ALONG/PERP)
([DISPLAY]/META)
Plots of the structure viewed perpendicular to or along
the various least-squares planes may be produced for inspection.
The graphics medium can be either the DISPLAY or the
META (i.e. EPS, HPGL or TEK4010) depending on the current setting.
PLOT NEWMAN ([DISPLAY]/META) (COLOR) (at1 at2)
NEWMAN plots are produced, provided that a CALC INTRA
instruction was carried out previously in order to prepare a file with
the relevant data for all Newman projections. The Newman plots may be
examined sequentially or for an individual one to be selected by
specifying the relevant central bond.
The graphics medium can be either the DISPLAY or the
META (i.e. EPS, HPGL or TEK4010) depending on the current setting.
PLOT ADP (RESD nr) (COLOR) ([DISPLAY]/META)
(OCTANT/[HETERO]/ENVELOPE) (LABELS/NOLABELS) (HATOM/NOHATOM)
(PARENT/NOPARENT) (MARGIN marg)
An Anisotropic Displacement Parameter plot (ADP) also
called thermal motion ellipsoid plot (ORTEP) is produced for residue
number nr (zero means all residues).
The COLOR option provides for the distinction of hetero
atom types in the plot (oxygen RED, Nitrogen BLUE and halogens GREEN).
The graphics medium can be either the DISPLAY or the
META (i.e. EPS, HPGL or TEK4010) depending on the current setting.
The overlap margin (cm., [0.08]) can be changed with
MARGIN marg.
The three plot angles xr, yr and zr to reconstruct the
present orientation are plotted in the lower right corner, upper left
corner and lower left corner respectively. The probability level of the
ellipsoid surfaces is shown in the upper right corner. When no VIEW
instruction was given previously, the program will calculate a minimum
overlap view.
Example: PLOT ADP 3 COLOR
BOX ([ON]/OFF) (RATIO ratio[1.333])
By default a drawing will be surrounded with a
rectangular box outline. The current setting of this feature may be
changed with the ON and OFF sub- keywords.
The corresponding clickable menu item is labeller
'decoration'.
The three numbers shown at the bottom right, top left and
bottom left corner of the box are the rotation angles xr, yr and zr
respectively with reference to the default setting. These numbers may
be used to reconstruct this particular orientation directly from the
default UNIT orientation via a VIEW XR xr YR yr ZR zr instruction.
The default horizontal to vertical size ratio of the box
for an ADP plot is 4/3. A ratio of 1 produces a square box.
Example: BOX ON RATIO 1.0
VIEW (UNIT) (XR xr) (YR yr) (ZR zr) ...
The current orientation of the molecule for plotting may
be modified with a VIEW instruction: VIEW XR 45 YR -55 will rotate the
molecule first clockwise about the horizontal X-axis, followed by an
anti-clockwise rotation by 55 degrees about the vertical Y-axis. VIEW
instructions are accumulative. The single keyword instruction VIEW will
bring the molecule back in the default orientation.
VIEW MIN/INVERT
MIN:Minimum overlap view based on least-squares plane
determined by the atoms included in the plot.
INVERT: The view matrix (and absolute structure is
inverted).
SET PROB (10/20/30/40/[50]/60/70/80/90)
The probability level for the ellipsoid surfaces is set
by default to 50%.
Example: SET PROB 30
SET WINDOW fraction
Set X-Window size to fraction
Example: SET WINDOW 0.6
SET LABEL SIZE size
Set the size of the atom labels from the current
size to the desired size (mm).
Example: SET LABEL SIZE 0.6
JOIN atom_name1 atom_name2 (DASH/LDASH)
Include an (optionally dashed )additional bond to the
bondlist for plotting. This provides an option to add bonds that are
not generated automatically on the basis of the join radii.
DETACH atom_name1 atom_name2
Delete specified connection from bondlist to be
plotted. This instruction is useful to delete unwanted connections in
the automatically generated bondlist.
Example DETACH Cu1 Cu2
DEFINE at1 TO at2 at3 .. atn (DASH/LDASH)
Include bond between at1 and the center of gravity of
the set at1-atn.
Such an instruction is usually executed automatically
to replace the original five 'covalent' metal to cyclopentadienyl
carbon bonds by a dashed bond from the metal to the center of gravity
of the ring.
Example: DEFINE Zn1 TO C1 C2 C3 C4 C5
RADII BONDS ((NORMAL/TO METAL/ TO H/ALL) bt r)/LIST
Sets bonds of specified type (i.e. NORMAL, TO METAL, TO
H or ALL) to another radius (r) and number of lines (related to the
value of bt) on the bond circumference or LIST current radii.
bt = bondtype should be within the range -5 to 5. Negative values
correspond with dashed lines
r = radius (Angstrom).
Example: RADII BONDS TO METAL 3 0.02
ELLIPSOID (C/H/OTHER) type (lines)
Set plottype of ellipsoids. Type = 0 or 1.
HINCLUDE/HEXCLUDE atomname1 .....
Facility to indicate H-atoms that should remain
'included' in the plotlist when the general (global) condition is
'no-hatoms'. The default setting is 'exclude'.
A HEXCLUDE instruction is therefore needed only to
undo an earlier HINCLUDE.
This feature is useful when only a few relevant
hydrogen atoms are to be displayed and the rest left out.
Example: HINCLUDE H601 H101
HELP (SPGR)
This instruction provides an on-line HELP facility.
The SPGR option lists all space groups known to PLATON.
LIST BONDS/ATOMS/SYMM/CELL/RADII
This provides for on-line inspection of BOND and
ATOM tables, the current symmetry, CELL dimensions and default radii.
LIST IPR/PAR (ival1 (ival2))
Intermal parameter values (see Appendix VII) may be
inspected with this instruction. A range will be listed when two values
are specified and the full range when none is given.
Example: LIST PAR 3 5
SET PAR p1 p2
This instruction is not meant for general use. It
provides a facility to modify internal parameter values, in particular
those with no equivalent (sub)keyword. p1 is the parameter number and
p2 the new value.
SET IPR p1 p2
This instruction is not meant for general use. It
provides a facility to modify internal parameter values, in particular
those with no equivalent (sub)keyword. p1 is the parameter number and
p2 the new value.
SET IGBL p1 p2
This instruction is not meant for general use. It
provides a facility to modify internal global parameter values, in
particular those with no equivalent (sub)keyword. p1 is the parameter
number and p2 the new value.
SAVE
This instruction causes the saving of subsequent
instructions on a file to be executed on all data sets, separated by
ENDS cards, on the parameter file.
See also SAVE
INSTRUCTION
END
This results in a normal end of program when the
.SPF file contains only one data set, otherwise the program restarts
for the next data set on the file.
QUIT
This results in an immediate stop of the program,
ignoring possible further datasets on the input file.
STOP
This results in an immediate stop of the program,
ignoring possible further datasets on the input file.
The atomic parameters (including unit cell
parameters, coordinates and temperature parameters) for a given
structure may be inputted in various ways:
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 free format.
TITL text
This text may be used for various titleing purposes.
It may be overridden at any time by another TITL instruction.
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.
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.
SPGR space-group-name
Space group symbol. See Appendix-IV 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 appendix - I.
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*K*(A*)(B*)+...)]
SUIJ atom_name sig(U11) sig(U22) sig(U33)
sig(U23) .. sig(U12)
Estimated standard deviations 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*K+...)]
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.
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 appendix I)
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 0.0i
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)...
Files with just positional parameters, not preceded by
CELL and symmetry cards are understood to be angstrom data. Coordinate
data may be preceded by an ANGSTROM card with optionally a
multiplication factor to transform the data to angstrom units. ATOM
cards may be as: C1 1.123 1.456 1.789.
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 (P212121)
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
A LATT card should precede any SYMM card in order that
the symmetry arrays are initialized 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
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-76
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.
Atomic radii used for covalent bonding etc.
-------------------------------------------
Ac 1.88 Er 1.73 Na 0.97 Sb 1.46
Ag 1.59 Eu 1.99 Nb 1.48 Sc 1.44
Al 1.35 F 0.64 Nd 1.81 Se 1.22
Am 1.51 Fe 1.34 Ni 1.50 Si 1.20
As 1.21 Ga 1.22 Np 1.55 Sm 1.80
Au 1.50 Gd 1.79 O 0.68 Sn 1.46
B 0.83 Ge 1.17 Os 1.37 Sr 1.12
Ba 1.34 H 0.23 P 1.05 Ta 1.43
Be 0.35 Hf 1.57 Pa 1.61 Tb 1.76
Bi 1.54 Hg 1.70 Pb 1.54 Tc 1.35
Br 1.21 Ho 1.74 Pd 1.50 Te 1.47
C 0.68 I 1.40 Pm 1.80 Th 1.79
Ca 0.99 In 1.63 Po 1.68 Ti 1.47
Cd 1.69 Ir 1.32 Pr 1.82 Tl 1.55
Ce 1.83 K 1.33 Pt 1.50 Tm 1.72
Cl 0.99 La 1.87 Pu 1.53 U 1.58
Co 1.33 Li 0.68 Ra 1.90 V 1.33
Cr 1.35 Lu 1.72 Rr 1.47 W 1.37
Cs 1.67 Mg 1.10 Re 1.35 Y 1.78
Cu 1.52 Mn 1.35 Rh 1.45 Yb 1.94
D 0.23 Mo 1.47 Ru 1.40 Zn 1.45
Dy 1.75 N 0.68 S 1.02 Zr 1.56
Note: OW is equivalent to O and Q1 is equivalent to C1.
Covalent radii are those given in the Cambridge
Structural data base manual.
The program contains internal integer and real
parameter arrays (IPR and PAR respectively). They include default
parameter settings and values that may be either explicitly or
implicitly manipulated with the (sub)keywords. Below is a list of some
of them. Their values may be changed with SET PAR and SET IPR
instructions or examined with LIST PAR and LIST IPR instructions. It
should be noted that there is no checking for side-effects.
IPR(141) - Nplane parameter in ADP
IPR(142) - Lines parameter in ADP
PAR(73) - Letter size
Positioning of Molecules in the Unit Cell
Molecules are positioned by default at a location in
the unit-cell with their centre of gravity within the range 0 to 1 and
closed (in Angstrom) to 0,0,0 [PAR(64), PAR(65), PAR(66)]
25-9-98