The platon crystallographic package - səhifə 46
Terminate parameter entry and start flipping.
1.4.32 – Analysis-of-Variance – SubMenu #0
184.108.40.206 – NorProbPlot
A Normal Probability Plot (Abrahams & Keve, 1971) of (Fobs
) / σ(Fobs
shown on the display. Expected is an almost linear curve with correlation coefficient,
intercept and slope about 1.0, 0.0 and 1.0 respectively. Deviations may indicate improper
weighting and systematic errors.
220.127.116.11 – Scatter Plot
A linear plot of Fobs
is created showing possible outliers.
18.104.22.168 – LogLog Plot
) versus Log(Fcalc
) plot is created showing possible outliers.
22.214.171.124 – StandardDev
A one sigma bar is added to Fobs
126.96.36.199 – END
Exit from Analysis of Variance routine.
Chapter 2 – The PLATON Tool
PLATON development as a molecular geometry tool started around 1980 as a non-menu
driven program. Instructions to the program were at that time entered interactively via the
keyboard. The current PLATON version translates mouse clicks on the menu into keyboard
instructions. Keyboard instructions can still be entered at the prompt on the PLATON menu.
Some of the less used instructions and options are available only as keyboard instructions.
This chapter details all the available instructions. The original non-menu mode is available
by invoking PLATON as '
This chapter also details the algorithms and notions
2.1 – Introductory Example
The following example, assumed to run in a terminal window, of the structure of SUCROSE
(neutron data) provides an introduction to the use of this program and its potential. The
structural parameters are assumed to reside in a free format disk file named
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
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
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 by entering the terminal command
platon -o sucrose.spf. This will load the data set
sucrose.spfand, since this file does not
contain an END instruction at the end of the file, the program comes back, after reaching the
end-of-file, with the prompt >> to receive more data and/or instructions via the keyboard. A
default calculation of the intra-molecular geometry may now be invoked with the instruction
CALC INTRA. The result of this calculation is written to a disk file (in this case
) along with some information as terminal window output. An analysis of short inter-
molecular contacts can be performed with a subsequent
CALC INTERinstruction. The
analysis may be completed with a
CALC COORDNinstruction that gives a listing of all
bonds and angles about all atoms (excluding C and H) involving atoms within a 3.6
Angstrom coordination sphere. A default anisotropic displacement ellipsoid plot
(commonly called ORTEP) is obtained by entering
PLOT ADP. The default plot
orientation can be rotated over 45 degrees about the vertical Y-axis by entering the
VIEW YROT 45in the terminal window. This instruction takes effect with a
PLOTinstruction. The session may be closed by twice entering the
ENDin the terminal window. All instruction should be entered in this non-menu
mode via the terminal window when invoked with the
-oflag,. A full list of instructions is
2.2 – On How it Works
This section on the program internals should provide a framework to understand the impact
of the available instructions. The input atomic coordinates (x, y, z) are with reference to
user-defined axes (
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
and C is normal to A and B. B will coincide with
bin monoclinic cells in the b-setting. If the
input axes are orthogonal, the two sets of axes
cand 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 standard uncertainties,
displacement parameters, a name (the embedded element type 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
for internal use and listed with their original label where possible.
A CALC instruction generally initiates a distance search on the basis of internal or user
supplied 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 the geometry
listing routine that tabulates 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 to allow the handling of the geometry of the complete molecule.
Care is taken, unless overruled, that all connected species have their center of gravity within
the bounds of the unit cell.
2.3 - Unit Cell Transformation
PLATON can be used to transform CELL, LATT, SYMM, SPGR, Coordinate and
Displacement Parameter data according to a specified transformation matrix.
The general format of the transformation instruction line is:
afs -> Meningoensefalit, meningoensefalit
afs -> Nb deze bovenstaande tekst wel weghalen!
afs -> Allergen Checklist for Food Suppliers or Manufacturers
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