The platon crystallographic package - səhifə 50
22.214.171.124 - CALC COORDN (atom_name (p1[3.6]))
The coordination geometry about a single atom may be examined with this instruction.
CALC COORDN O3 3.2
126.96.36.199 - CALC METAL (p1)
Distances between metal atoms less than p1 (default 5.0 Angstrom) are calculated. This
option is included in the default CALC calculations.
CALC METAL 10.0
188.8.131.52 - 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
184.108.40.206 - 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.
CALC DIST I 4.0
220.127.116.11 - 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.
18.104.22.168 - ANGL Atom_name1 Atom_name2 Atom_name3
The angle between the specified and not necessarily bonded atoms is calculated.
22.214.171.124 - TORS Atom_name1 Atom_name2 Atom_name3 Atom_name4
The dihedral angle involving the four specified atoms (not necessarily bonded) is calculated.
126.96.36.199 - LSPL Atom_name1 Atom_name2 Atom_name3 Atom_name4 ...
The least-squares plane determined by the specified atoms is calculated.
2.5.3 - Graphics Related Instructions
PLATON provides graphics options to support the geometry analysis. A number of options
are supported only from the menu (STEREO, MONO).
188.8.131.52 - 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. PostScript or HPGL)
depending on the current setting.
184.108.40.206 - PLOT NEWMAN ([DISPLAY]/META) (COLOR) (at1 at2)
Newman plots are produced. 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. PostScript, HPGL) depending on the current
220.127.116.11 - 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) 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.
PLOT ADP 3 COLOR
18.104.22.168 - 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 labelled '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.
BOX ON RATIO 1.0
22.214.171.124 - 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.
126.96.36.199 - 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).
188.8.131.52 - SET PROB (10/20/30/40//60/70/80/90)
The probability level for the enclosing ellipsoid surfaces is set by default to 50%.
SET PROB 30
184.108.40.206 - SET WINDOW fraction
Set X-Window size to
SET WINDOW 0.6
220.127.116.11 - SET LABEL SIZE size
Set the size of the atom labels from the current size to the desired size (mm).
SET LABEL SIZE 0.6
18.104.22.168 - JOIN atom_name1 atom_name2 (DASH/LDASH)
nclude an (optionally dashed) additional bond to the bond list for plotting. This provides an
option to add bonds that are not generated automatically on the basis of the JOIN RADII
calculations. The difference between DASH and LDASH is the number of lines drawn on
the dashed bond.
22.214.171.124 - DETACH atom_name1 atom_name2
Delete the specified connection from the list of bonds to be plotted. This instruction is
useful to delete unwanted connections in the automatically generated bond list.
DETACH Cu1 Cu2
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