The platon crystallographic package - səhifə 57
ARU gives the list of molecules.
STATUS list various parameter settings and other relevant data.
SYMM gives a list of all equivalent positions, preceded by their internal sequence number
that is used in conjunction with the ARU instruction.
TYPES gives a listing of all atom-type dependent setting such as radii and colours. If none
above keywords is given, all the information is shown.
Example: LIST ATOMS BONDS
3.5.37 - LIST ATOM (atom-name/atom-type/INTER)/(RESD resdnr)
This lists atom data from the atom list for the specified atom or atom-type.
LIST ATOM O
3.5.38 - LIST BOND (atom-name1/atom-type atom-name2/atom-type/INTER)/ (RESD resdnr
This lists bond data for the specified bond from the bond list.
LIST BOND C3 C4
3.5.39 - LIST CELL
This displays the current cell parameters for inspection.
3.5.40 - LIST SYMM
List symmetry operations and related data.
3.5.41 - LIST PAR (nr1 (nr2))
Option to list an internal parameter value held in the PAR list. A range is listed when two
numbers have been specified or the full list is case that none was specified. New values may
be assigned with the SET PAR instruction.
LIST PAR 5
3.5.42 - LIST IPR (nr1 (nr2))
Option to list an internal parameter value held in the IPR list. A range is listed when two
numbers have been specified, or the whole list is case of no range specification. New values
may be assigned with the SET IPR instruction.
LIST IPR 3 5
3.5.43 - MONO (PERSP d)
A single perspective drawing is to be produced as seen from a point at d cm. along the ZP
axis, above the centre of the drawing. The default setting is 10000 cm. (effectively infinity)
but may be set to 60 cm. for convenient perspective viewing. The actual value is plotted in
the top right corner of the plot (zero for infinite perspective) to avoid confusion.
3.5.44 - NOMOVE([ON]/OFF)
3.5.45 - NOSORT
No atom list sorting toggle.
3.5.46 - OMIT OUTSIDE (xmin xmax ymin ymax zmin zmax/atom-name r/0)
All atoms with their centres outside the box defined by the fractional coordinates
xmin,...,zmax are omitted from the drawing, together with any bonds to them. This is useful
as a 'window' on a packing diagram. The window may be reset by another OMIT OUTSIDE
instruction, or cancelled alltogether by OMIT OUTSIDE 0. Note that molecules lying across
the edge of the window will be drawn incomplete. An alternative option is the exclusion of
all atoms with their centres outside a sphere with radius r around a specified atom.
OMIT OUTSIDE C(1) 5
OMIT OUTSIDE 0.5 1 0.5 1 -.25 .25
3.5.47 - OMIT aru .../resd
Omit the specified items from the 'plot-list'.
3.5.48 - ORGA
Set default parameters for type organic structure.
3.5.49 - OVERLAP (MARGIN mrg[0.10]) (SHADOW shad[0.10])(ON/OFF)/BA/BB[ON]
The overlap margin (non-bonded bond-bond, atom-atom, atom-bond overlap) is set by
default to the value mrg = 0.1 cm and the incoming bond shadow margin to shad = 0 cm.
Overlap calculations (by default) may be turned off for fast testruns. This should be
specified before plotting and after the specification of the plot-style.
3.5.50 - PACK (RANGE xmin xmax ymin ymax zmin zmax (atom-name))
This causes a search for all ARU's having their centres inside the box defined by the
fractional coordinates given. By default PACK RANGE displays the contents of a unit cell.
However, this will not show the complete packing arrangement of the crystal; it is necessary
to supply a range that will ensure that a pair of translated molecules will be found in each
axial direction. This is achieved by giving a range of cell translations. In most structures, the
result of a range of two in each axis is usually too congested to be of any use, so that it is
best to restrict the range to one on the axis closest to the view direction.
PACK RANGE -0.5 1.5 -.5 1.5 0 1
might be appropriate for a z-axis projection. The instruction PACK generates by default all
ARU's with their centre within the unit cell.
The ARU's that obey the conditions are added to the ARU list. The ARU list is reset to ARU
UNIQUE at the beginning of the search. No other lists are affected. The ARU list may be
displayed by the LIST ARU instruction.
3.5.51 - PACK PLAN h k l d1 d2 RANGE xmin .. zmax (atom_name)
ARU's are put in the moles list that satisfy the condition of lying within the range
xmin,...,zmax and in the neighborhood of the specified hkl-plane (d1 and d2 are in
PACK PLAN 1 1 1 -.5 .5 RANGE -1 2 -1 2 -1 2
3.5.52 - PLOT (DISPLAY/META) (LIST) (MOGLI)
This produces a drawing using the information set up by the previous instructions on either
the current graphics medium (default) or on the specified medium (Display, Plotter or Meta-
file). The default medium is either the one previously set or the display by default. An
automatic JOIN RADII UNIQUE EXPAND instruction is executed when no previous JOIN
instruction was given and a VIEW MIN instruction is case of no previously given VIEW
instruction. The MOGLI option may be used to generate DGE and OBY files to be used to
view the molecule in 3D with the PSSHOW program of the MOGLI package on a PS300
display (use PLOT CAL MOGLI to generate the files without display or plotter output).
The special instruction PLOT CAL 3 will generate a file with full 3D vector information for
a ROD-style plot, independent of previous parameter settings.
3.5.53 - PUT atom-name/atom-type/OR/OA/OB/OC position (atom-name/atom-
type/OR/OA/OB/OC position .. )
N, NE, E, SE, S, SW, W, NW, NUCL, AUTO
The automatic label positioning routine considers eight (or nine in the case of SOLID
NUCL) possible positions for each label. These are conveniently designated by the compass
directions N, NE, E, SE, S, SW, W, NW (or NU). The PUT instruction forces particular
atom labels into positions chosen explicitly by the user. Atoms named here are positioned
first, then the automatic routine places the rest. A position may also be given as AUTO, so
that all atoms of a given type can be fixed and then specific exceptions made:
PUT C SE C12 W C14 AUTO
PUT instructions must follow LABEL. They will be ignored if they precede it.
3.5.54 - QUIT
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