1.4.7.20 - MinDistCrit
'Q-peaks' at a distance shorter than a preset distance to a neighbor are deleted from the input
for clarity. By default this distance is 1.0 Angstrom. The clicking positions give (from left to
right) 0.00, 0.25, 0.50. 0.75 & 1.0 Angstrom.
1.4.7.21 - (IN/EX)CLUDE ZOMBIE
This feature in/ex-cludes hydrogen bonds sticking out to ghost-atoms.
1.4.7.22 - AutoMolExpand TOGGLE
Toggle for auto molecule expand along with ARU add or ARU delete. This toggle is OFF
(i.e. no Expand) for polymers and ON for molecules by default.
1.4.7.23 - PREV/NEXT TOGGLE
Toggle to proceed to previous or next entry on a multi-entry CIF or FDAT file.
1.4.7.24 - ENTRY LISTon Multiple entry file (e.g. FDAT, CIF)
Clicking on the Menu Option
ENTRY LIST or with the keyed instruction
ENTRY a listing
of all entries in a CIF or FDAT file will be presented. Specific datum entries can be selected
either by their sequence number or by name from this list as keyboard instructions.
Examples:
ENTRY 3
ENTRY SUKCUC
1.4.7.25 - Reset & END Buttons
RESET returns the display to a default STICK presentation of the molecule(s).Return to
main PLATON menu with
END
1.4.8 – OPTEP SUB-MENU # 1
1.4.8.2 - DISPLAY TEXT
Toggle for the display of auxiliary textual material.
1.4.8.3 - NEW TEXT
Toggle for the acceptance of new text. The 'NewText' button will turn RED by clicking on
it. A text string can now be typed and shown in the upper right corner of the canvas (after a
CR) with the current character size shown in the lower left part of the canvas. Text can be
moved to the desired position with
MoveText
.
1.4.8.4 - MOVE TEXT
When active (i.e. RED), clicking on a text item will make it disappear to reappear at the
position of a second click.
1.4.8.5 - TEXT SIZE
The current character size is changed on the basis of the click position. New text items will
be draw with the new character size. The character size of existing text may be changed to
the current size by clicking on them in the 'ChTextSize' mode on (i.e. RED).
1.4.8.6 - DELETE TEXT
Text items can be deleted by clicking on them in the 'DeleteText' on (RED) mode.
1.4.8.7 - CHANGE TEXT SIZE
When ChTextSize is on (RED), clicking in text items will change their character size to the
current default.
1.4.8.8 - CoordRadDef
By default, the maximum distance for the calculation on the coordination geometry about an
atom is 3.6 Angstrom. Clicking in one of the sub-menu boxes will change the default value
to 3.0, 4.0, 5.0 or 6.0 Angstrom.
1.4.8.9 - NOSYMM TOGGLE
When Active (i.e. RED), No symmetry expansion is done in the geometry calculations. This
toggle has effect only when activated before any explicit or implied CALC INTRA
instruction is executed. No symmetry expansion can be useful when the application of
symmetry relations results into undesired infinite networks in the subsequent analysis.
Similarly, undesired infinite chain expansion is avoided in the ORTEP display.
1.4.8.10 - VIEW INVERT
Invert image (i.e. change absolute structure).
1.4.8.11 - COLOR TYPE
Toggle for changing the color assignment for atom-types in ORTEP displays. The clicking
position indicates the color to be assigned from the set (BLACK, RED, GREEN,
BLUE,YELLOW, ORANGE, VIOLET, BROWN). The related keyboard instruction
COLOR TYPE element color.
1.4.8.12 - ALTERNATIVE RASTER3D STYLE
Alternative Raster rendered ORTEP option.
This option requires an accessible
raster3d
implementation.
Four plot styles are available and invoked depending on the click position.
1. stick presentation (no ellipsoids)
2. opaque ellipsoid presentation
3. main axes planes of the ellipsoids only
4. main axes planes + transparent ellipsoids.
Two files are generated
1.
A PDB-styled file (extension:
.rst) with ATOM and ANISOU records
2.
A file (extension:
.r3d) suitable to run the program 'render' of the Raster3D package.
1.4.8.13 - ORTEP - HETERO ELLIPSOIDS
Hetero atom octants are shaded (3D ellipsoids) to clearly distinguish then from carbon atoms.
The click position determines whether H-atoms are drawn with two of three dimensional outline.
1.4.8.14 - ENVELOPE STYLE ELLIPSOIDS
Display of projected outline of displacement ellipsoids only.
1.4.8.15 - OCTANT STYLE ELLIPSOIDS
Octant 3-D ellipsoids for all non-hydrogen atoms. The click position determines whether
two or three dimensional outlines for H-atoms are drawn.
1.4.8.16 - PARENTHESES
Toggle for include/exclude parentheses of ORTEP labels. This toggle operates
independently from the parentheses usage in listings.
1.4.8.17 - DISPLAY BY RESIDUE
This button contains NRES (= number of species) + 1 clickable boxes. By default, all
residues are drawn. This corresponds to the leftmost click position. The other click positions
bring up individual residues. The number of the residue displayed is shown on the drawing.
The number 0 indicates that all residues are shown.
1.4.8.18 - NrLinesNorm
The click position determines the number of lines drawn in a bond involving non-hydrogen
and non-metal atoms.
1.4.8.19 - NrLinesToMe
The click position determines the number of lines drawn for bonds to Metals.
1.4.8.20 - RadBndAll
Change Default Bond radii for All Bonds.
For More Details on RADII BONDS
1.4.8.21 - RadBndNorm
Change Default Bond radii for Normal Bonds.
For More Details on RADII BONDS
1.4.8.22 - RadBndToMet
Change Default Bond radii for bonds to Metals.
For More Details on RADII BONDS
1.4.8.23 - RadBndToHat
Change Default Bond radii for bonds to H-Atoms
For More Details on RADII BONDS
1.4.8.24 - BondTaper
The click position determines the degree of bond taper
1.4.8.25 - PLUTON & END BUTTONS
Clicking on the PLUTON button provides a direct pathway to PLUTON sporting the same
connectivity and orientation etc. Return to main PLATON menu with 'END'.
1.4.9.2 - X-LineWidth Toggle
