The platon crystallographic package - səhifə 53
of dummy cell edges). A second, orthogonal system (A, B, C) (see J.D. Dunitz, X-Ray
analysis and the Structure of Organic Molecules, Cornell University Press, p235) with
coordinates (XO,YO,ZO) in Angstroms is set up internally: The unit vector A is choosen
along a, B as unit vector normal to a in the ab plane, and C normal to A and B. This
orthogonal system is coincident with the first system when the input axes are orthogonal.
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.
Each connection is simply a pair of atom serial numbers referring to the input atom list.
Some JOIN instructions also find connections between input atoms and other atoms related
to the original list by crystallographic symmetry. This may include both connections to a
symmetry related part of a molecule sitting on a special position or intermolecular
connections. In order to store these connections for plotting, the program appends dummy
symmetry-generated atoms to the atom list and marks them with a special flag.
If the final picture is to contain several molecules, as in a packing diagram, or a complete
molecule for which the input atoms represent only the symmetry-independent portion of it
when a molecule lies in a crystallographically special position in the unit cell, the program
will have to generate XP, YP, ZP coordinates for the atoms in each of these molecules or
symmetry-related molecular fragments. This is controlled by two further lists: a list of
symmetry operations pertaining to the structure, input directly with SPGR, LATT or SYMM
instructions atoms are input to the program, they are stored both in the X, Y, Z and the XO,
YO, ZO coordinate system. The XP, YP, ZP system is used only when plotting is actually
being performed. Each atom has additional information stored for it including the atom
name (the embedded element name is used by default to set various radii) and various flags
such as for inclusion in the plot and labeling. This data structure is known as the atom list.
Duplicate entries with the same coordinates are skipped from the input stream.
The JOIN instructions (either by default or as specified) set up a list of connections (known
as bond structure, input directly using the SPGR or LATT and SYMM instructions; and a
list of 'molecules and ions' (known as ARU list) to be drawn.
The program works as follows. Instructions (free format) are read and interpreted. Various
instructions add to the list of atoms and symmetry operators. The JOIN instructions set up
the connections list and may also add to the atom and ARU-lists if connections between
ARU's are to be generated. Plotting parameters are then set by user instructions or left at
default settings. No plotting is actually done until the PLOT instruction is read. This first
sets up the XP, YP, ZP plotting list of all atoms to be plotted. The information in the ARU
list and the current view matrix together tell the program how to convert X, Y, Z into XP,
YP, ZP. The plotting coordinates and atom radii are scaled from Angstroms to cm. and
corrected for perspective if requested. In the non-stick mode, all atoms in the plotting list are
drawn, allowing for obscuring of some by others and bonds, and intersection of spheres in
space-filling models and bonds in the ROD mode, except that dummy atoms are not usually
drawn - they are required only so that connections between molecules are possible, and will
generally be duplicated by other non-dummy atoms generated in the XP, YP, ZP list by
symmetry from the original input atoms. Following the atoms, all the bonds are drawn,
omitting portions obscured by atoms or bonds. Atoms are labelled by a routine which
minimises overlap of the labels by atoms, bonds and other labels. When the picture is
complete, the next instruction may be read.
Most data are stacked in a large array, either bottom-up or top down, so that the stack size is
the limiting factor for the size of the problem that the program can handle. The program
reports on the maximum memory usage in the current run. The stack size is a program
The input list of atoms is checked on redundancy.
DATA and INSTRUCTION FILES
The order in which data are read is as follows:
- The primary datafile (e.g. sucrose.spf) is read. When an EOF or ENDS line is
- A file named sucrose.def (when present) is read.
- Saved Instructions are read
Instructions from the keyboard or Mouse-clicks are processed
3.4 - Terms and Notions.
Connected sets of atoms are assembled in the following way. The procedure is started by
first fixing a suitable atom. Next symmetry operations are performed on all atoms in the
input set to find atoms that are connected to it. Atoms that are found to be connected are
fixed as well and used to fix yet other, possibly symmetry transformed, atoms bonded to
them as well. This procedure continues until no new bonded atoms are found. In the simple
case of one chemical unit per asymmetric unit this constitutes an object named a molecule
and is denoted with the identity code 1555. Symmetry related molecules are denoted by the
general code sklm, where s is the number of the symmetry operation of the space group and
k,l and m translation components. Chemical units may extend over more than one
asymmetric unit. They may have a symmetry element that coincides with the space group
symmetry such as an inversion centre or a screw axis. In such cases we will find atoms in
the above search for a connected set of atoms that are bonded to the connected set at a
position different from the one that was fixed in view of an earlier connection. Those atoms
are added to the connected set and marked as symmetry related. The symmetry operation of
this atom with respect to the primary one is coded and added to the molecule (aru) list. A
chemical unit around an inversion centre thus consists in the PLUTO78 terminology of two
molecules: 1555 and 2555. A further complication may be the presence of more than one
crystallographically independent chemical unit in the unit cell (including solvent molecules
and anions). In that case not all atoms will be fixed when the above procedure comes to an
end when no more connected atoms are found. In that case a new residue is started by again
arbitrarily fixing a suitable atom and expanding it to a connected set. A particular residue r
within a molecule is indicated with the code sklm.rr (e.g. 3564.03). It is understood that the
code without a fraction stands for the full collection of residues. Thus in the case of two
residues the molecule code 2562 is equivalent with the two residue codes 2562.01 and
2562.02. In order to be more precise two new terms have been introduced in PLUTON and
PLATON. The basic structural unit is the asymmetric residue unit ( = ARU) coded as
sklm.rr. A molecule (ion) will will be an assembly of at least one aru. The set of aru's
making up the asymmetric structural unit are called asu and encoded as sklm.
Disorder. Based on the supplied population parameters an attempt is made to suppress
bonds between disorder parts with unequal population parameter values.
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