PLATON - MANUAL PLATON - MANUAL
PLATON HOMEPAGE
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.
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.
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.
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 etc.
Example: a' = b + c is encoded as 0 1 1
t1 t2 t3 indicate a shift of origin after the cell transformation. The shift vector is substracted from the transformed coordinate data.
A TRMX (or the synonymous) TRNS intruction may contain either 3 numbers (i.e. translation only), 9 numbers (i.e. transformation matrix only) or 12 numbers (i.e. both transformation and shift)
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
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
Example: shelxl.res structured input file on example.spf (with the instruction TRNS -2.666 inserted)
invoked with platon example.spf and instructions CALC SHELX and END
TITL Nardelli (Sucrose)
CELL 0.71073 10.8633 8.7050 7.7585 90.000 102.945 90.000
ZERR 1 0.0005 0.0004 0.0004 0.000 0.006 0.000
LATT -1
SYMM - X , 0.50000 + Y , - Z
SFAC C H O
UNIT 24 44 22
FVAR 1.00000
TRNS -2.666
O2 3 0.22954 0.43550 0.74766 =
11.0000 0.0277 0.0288 0.0193 -0.0013 0.0084 -0.0031
O1 3 0.17143 0.34630 0.39165 =
11.0000 0.0154 0.0131 0.0177 0.0006 0.0035 -0.0002
O3 3 0.30801 0.74770 0.70279 =
11.0000 0.0328 0.0252 0.0478 -0.0172 0.0206 -0.0099
etc ...
H611 2 0.36724 0.01189 0.11947 =
11.0000 0.0422 0.0592 0.0661 0.0164 0.0189 0.0216
HKLF 4 1 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000
will produce a new file example.res
TITL Nardelli (Sucrose)
CELL 0.71073 10.8633 8.7050 7.7585 90.000 102.945 90.000
ZERR 1 0.0005 0.0004 0.0004 0.000 0.006 0.000
LATT -1
SYMM - X , 0.50000 + Y , - Z
SFAC C H O
UNIT 24 44 22
FVAR 1.00000
O1 3 0.82857 1.84630 0.60835 =
11.0000 0.0154 0.0131 0.0177 -0.0006 0.0035 0.0002
O2 3 0.77046 1.93550 0.25234 =
11.0000 0.0277 0.0288 0.0193 0.0013 0.0084 0.0031
O3 3 0.69199 2.24770 0.29721 =
11.0000 0.0328 0.0252 0.0478 0.0172 0.0206 0.0099
Etc ...
H611 2 0.63276 1.51189 0.88053 =
11.0000 0.0422 0.0592 0.0661 -0.0164 0.0189 -0.0216
HKLF 4 1 1.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 1.0000
Where the symmetry operation 1-x,3/2+y,1-z was applied to O1. All other atoms are transformed (in this case with the same operation) to make a connected molecule.
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.
The logical order of calculations is intra-molecular, inter- molecular and coordination geometry.
In the description of individual instructions below the following applies:
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.
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
By default, the numerical part of an atomic label will be enclosed within parentheses.
Example: PARENTHESES 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
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
The elements in the exclude list will be excluded from all calculations.ELn may be Met for metal.
Example: EXCLUDE H
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
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 at the start of the subsequent calculations. Alternatively, the same data could be supplied as on the CALC HBONDS instruction.
D-H distances will be normalised to standard values when the keyword NORM is included. Their default settings may be changed with SET PAR instructions.
The current hbond criteria and normalisation values with associated SET PAR numbers are:
Example SET PAR 298 0.97 to mormalise O-H on 0.97 Angstrom.
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.
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.
Explicit line specification between two not necessarely bonded atoms.
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:
A PLUTON window is brought up with a display of the fit.
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
In the interactive mode, an automatic fit will be attempted with the specification of two residue numbers
Example: FIT 1 2
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 CALL ADDSYM, CALC INTRA, CALC INTER, CALC COORDN and CALC METAL, CALC SOLV.
The default instruction CALC INTRA produces a full calculation and listing of all intra-molecular geometrical parameter options relevant for the structure at hand using default covalent radii drawn from internal tables.
Atoms with distances less than the sum of their covalent radii plus a tolerance TOLA (Default = 0.4 Angstrom) are considered to be bonded. The default radii values may be modified by explicit specification (in which case the default for TOLA is set to zero, unless specified explicitly). Alternatively the parameter TOLA may be modified in order to include longer distances as bonds.
Example: CALC INTRA O 1.0 C 0.8
Sub-Keyword Options:
Alternatively, this parameter can be set with a SET PAR instruction:
Example: SET PAR 16 2.5
Example: CALC INTRA NOLSPL NORING
The search for rings (default up to 24-membered) can be limited to 6 with the instruction SET IPR 219 6 before the CALC INTRA instruction.
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
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. (Rmax = 25 by default).
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.
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.
The parameters p1,p2 & p3 are the same as described for the HBOND directive.
Specification of the sub-keyword NONA will suppress the network analyses section of the H-Bond calculation.
The search for hydrogen bonds is by default done only for the full weight or major disorder atoms. The sub-keyword DISORDER may be used to include minor disorder positions as well in the analysis.
This instruction gives an analysis of the coordination sphere for the atom types specified with El1 etc. Bond distances and bond angles are calculated for atoms within the specified radii.
By default (i.e. no specific options and data specified) such a calculation is done for all atom types, excluding C and H, and with a radius of 3.6 Angstrom. This default radius may be changed with the specification of the desired value p1.
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 TBA = 150 degree).
Example: CALC COORDN 4.0 NOANG
Example: CALC COORDN P 3.0 FIVE
The coordination geometry about a single atom may be
examined with this instruction.
Example: CALC COORDN O3 3.2
Distances between metal atoms less than p1 (default 5.0 Angstrom) are calculated. This option is included in the default CALC calculations.
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.
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
With this option a distance between two specified and not necessarily bonded atoms may be calculated between atoms in the atom_array.
The angle between the specified and not necessarily bonded atoms is calculated.
The dihedral angle involving the four specified atoms (not necessarily bonded) is calculated.
The least-squares plane determined by the specified atoms is calculated.
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.
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.
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
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
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.
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).
The probability level for the ellipsoid surfaces is set by default to 50%.
Example: SET PROB 30
Set X-Window size to fraction
Example: SET WINDOW 0.6
Set the size of the atom labels from the current size to the desired size (mm).
Example: SET LABEL SIZE 0.6
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.
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
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
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
Set plottype of ellipsoids. Type = 0 or 1.
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
This instruction provides an on-line HELP facility. The SPGR option lists all space groups known to PLATON.
This provides for on-line inspection of BOND and ATOM tables, the current symmetry, CELL dimensions and default radii.
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
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.
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.
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.
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
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.
This results in an immediate stop of the program, ignoring possible further datasets on the input file.
This results in an immediate stop of the program, ignoring possible further datasets on the input file.
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.
This text may be used for various titleing purposes. It may be overridden at any time by another TITL instruction.
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.
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.
Space group symbol. See Appendix-IV for more details.
First parameter specifies the Bravais lattice type and the second whether the lattice is acentric or centric.
Symmetry operation. See appendix - I.
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.
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*)+...)]
Estimated standard deviations for the anisotropic thermal parameters.
Isotropic temperature factor along with its associate standard deviation.
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.
[
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
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. (see appendix I)
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)
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)...
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.
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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)]
PLATON HOMEPAGE