'setenv RASEXE '/usr/local/bin/rasmol'
1.4.5.25 - Reset & END BUTTONS
Clicing on RESET will bring the display back to a default STICK plot of the molecule(s).
Return to main PLATON menu with
END
1.4.6 – PLUTON SUB-MENU #4 (Geom)
1.4.6.2 - Distance Calculation
This option provides interactive distance calculation between two labelled atoms by clicking
on them. The two atoms are not required to be bonded. Both atoms should be addressable
i.e. listed in the primary atom list as shown with the
LIST ATOMS instruction. When a
clicked atom is not yet in this list, it will be added automatically. The added atoms are now
available for distance calculation (i.e. reenter the DIST instruction) and their label shown.
Note: No s.u.'s are available with this option. Use the ORTEP link instead when s.u.'s on
bonds are needed as well.
1.4.6.3 - Angle Calculation
This option provides for the interactive calculation of an angle involving three atoms (not
necessarily bonded) by clicking on the three atoms involved. Note: Clickable atoms are
those included in the primary atom list. This list can be inspected using the
LIST ATOMS
instruction.
1.4.6.4 - Torsion Angle Calculation
Option for interactive calculation of torsion angles between named atoms by clicking on
them in the desired order. The atoms involved need not to be bonded. Note: The clickable
atoms are those included in the primary atom list. This list can be inspected using the
LIST
ATOMS instruction.
1.4.6.5 - GeomCalc
This option allows for the display of bond distances and angles around an atom by clicking
on it. Clickable atoms are those included in the primary atom list. This list can be inspected
with the
LIST ATOMS instruction.
1.4.6.6 - LIST TYPES
Info on the data associated with the atom types in the structure is displayed for inspection.
Example:
ATOM TYPES AND PARAMETERS
( May be Changed with COLOR TYPE, BWC TYPE or RADII ATOMS instructions)
====> COLOR TYPE atom-type col (atom-type col ...)
col = BLACK(WHITE), RED, GREEN, BLUE, YELLOW
ORANGE, VIOLET, BROWN, NONE
====> BWC TYPE atom-type bwc (atom-type bwc ...)
bwc = CONTOUR, NET, SHADE, SEGMENT, DOTS, BLACK, CROSS, PARALLEL, GLOBE,
MERIDIAN, HORIZONTAL, VERTICAL, MESH, DIAGONAL, SLANT, TEXTILE, VOID
NR TYPE COLOR BWC VDW- COV- JOIN- PLOT-RAD (TOL = 0.2
A/atom)
================================================================================
1 H NONE VOID 1.20 0.23 0.43 0.12
2 C BLACK SHADE 1.70 0.68 0.88 0.20
3 O RED BLACK 1.52 0.68 0.88 0.20
4 N BLUE NET 1.55 0.68 0.88 0.20
1.4.6.7 - LIST LINES
Clicking on this option generates a summary of data associated with the various bond types
for inspection.
Example
Bond(s) Radius(Ang) Lines Dash
Normal 0.120 2 0
Intermolecular 0.020 5 1
To H 0.120 2 0
1.4.6.8 - LIST ARU
Clicking on this option generates a display on the alpha-numeric window of the list of
ARU's and their attributes for inspection.
Example:
Asymmetric Residue Units :: UNIQUE = 2, INTER = 0, TOTAL = 2
The first 1 refer(s) to 1555.nn ARU's, the next ones to _a, _b etc
Resd# ARU AtomColor PatternColor BondColor #Lines
1 1555.01 - - - 0
2 3575.01 - - - 0
(Partially) ACTIVE Asymmetric Structure Units = 2
1555. 3575.
1.4.6.9 - LIST FLAGS
List Flags associated with atoms for inspection.
1.4.6.10 - LIST CELL
Cell dimensions for the current unit cell are displayed for inspection.
1.4.6.11 - LIST SYMM
S
ymmetry operation for the current structure are displayed on the alpha-numeric window
(where PLATON was invoked).
1.4.5.12 -
LIST ATOMS
The list of atoms (coordinates and frags) for the atoms in the asymmetric structural unit is
displayed on the alpha-numeric screen for inspection.
1.4.5.13 - LIST BONDS
Bonds and associated info for the bonds in the asymmetric structural unit are displayed on
the alpha-numeric display for inspection.
1.4.6.14 - PLOT RESIDUES - Select Residue(s) for Display
Either the complete set of residues (by clicking in the leftmost box) of individual residues
may be displayed (by clicking in one of the other boxes). The number of boxes equals the
number of residues (molecules) + 1.
1.4.6.17 - LABEL ATOMS TOGGLE
Global atom labeling toggle. Clicking on the right box will also include H-atoms in the
labeling.
1.4.6.18 - ENTRY LIST
Listing of the entries in the input file.
1.4.6.19 - STEPWISE ROTATION ABOUT Z
Stepwise rotation about Z (perpendicular to image). Clicking in the central area gives small
rotation steps. Clicking further from the center corresponds with larger rotation steps.
Clicking left from the center or right from the center determines the sense of rotation.
1.4.6.20 - STEPWISE ROTATION ABOUT Y
Stepwise rotation about the horizontal axes (Y). Clicking in the central area gives small
rotation steps.Clicking further from the center corresponds with larger rotation steps.
Clicking left from the center or right from the center determines the sense of rotation.
1.4.6.21 - STEPWISE ROTATION ABOUT X
S
tepwise rotation about the horizontal axes (X). Clicking in the central area gives small
rotation steps.Clicking further from the center corresponds with larger rotation steps
Clicking left from the center or right from the center determines the sense of rotation.
1.4.6.22 - COLOR OPTIONS
The assignment of color to plot-items can be done at four levels.
1 - Global Color
2 - Per Atom-type
3 - Per Residue-type
