ARU green 1565.01
ARU-related colors are displayed with:
COLOR ARU (on/off)
or by clicking the 'col ARU' menu field
This option may be combined with the 'Black-and-White' Patterns:
BWC (on/off)
1.4.4.23 - DefineToEnd
With this option, a set of bonds originating from a central atom to selected atoms will be
replaced by a dash line to the corresponding centre of gravity.
In general, this function will be used for bonds between a metal and atoms partaking in a
unsaturated system (e.g. a C=C bond).
Procedure:
1) Click on the 'Define' menu box.
2) Click on base atom ( in general a metal)
3) Click on the atoms determining the centre of gravity to which a substituting dashed
bond has to be drawn.
4) Click on the 'End' field.
Alternatively issue the keyboard instruction:
DEFINE at1 TO at2 at3 at4 at5
1.4.4.24 - JoinDashDetach
Toggle for interactive JOIN, JOIN DASH and DETACH operations.
The corresponding keyboard instructions are:
(3.5.32) - JOIN/DETACH (DASH) Atom_name1 Atom_name2 (radius number_of_lines)
1.4.4.25 - Reset & END BUTTONS
The RESET instruction will bring the display back to a default STICK style plot of the molecule(s).
Return to main PLATON menu with END
1.4.5 – PLUTON SUB-MENU #3 (View)
1.4.5.2 - VIEW UNIT
UNIT orientation matrix, i.e. XO horizontal, YO vertical (up) and ZO pointing to the
viewer.
1.4.5.3 - VIEW MIN
Minimum overlap orientation (i.e. the major inertial axes are horizontal and vertical
respectively).
1.4.5.4 - VIEW XO
VIEW down XO. YO and ZO are horizontal and vertical (up) respectively.
1.4.5.5 - VIEW YO
VIEW down YO. ZO and XO are horizontal and vertical (up) respectively.
1.4.5.6 - VIEW ZO
VIEW DOWN ZO. XO and YO are horizontal and vertical (up) respectively.
1.4.5.7 - VIEW AFACE
VIEW From [1,1,1] to [0,1,1]
1.4.5.8 – VIEW BFACE
VIEW From [1,1,1] to [1,0,1]
1.4.5.9 – VIEW CFACE
VIEW From [1,1,1] to [1,1,0]
1.4.5.10 – VIEW INVERT
An inverted image with respect to the current image is obtained with this instruction.
1.4.5.11 - VIEW LINE
View direction defined by two atoms. The associated two atoms can be entered by clicking
on the centre of the corresponding atoms is the plot.
1.4.5.12 - VIEW PERP
View perpendicular to three named atoms. The three atoms may be indicated by clicking on
their centres in the plot.
1.4.5.13 - VIEW BISECT
VIEW direction defined by the bisector of the angle atom1-atom2-atom3. The three atoms
may be selected by clicking on the centers of the associated atoms in the plot.
1.4.5.14 – Select Residue PLOT
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.
1.4.5.17 - LABEL ATOMS TOGGLE
Global atom labeling toggle. Clicking on the right box will also include H-atoms in the
labeling.
1.4.5.19 - Stepwise Rotation About Z
Stepwise rotation about Z (perpendicular to image). Step size and direction based on click
position.
1.4.5.20 - 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.
1.4.5.21 - Stepwise Rotation About X
Stepwise rotation about the horizonatal 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.
1.4.5.22 - 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
4 - Per ARU
Option 1:
Instruction:
COLOR BLACK/RED/GREEN/BLUE/YELLOW/ORANGE/VIOLET/BROWN
Option 2:
Color assignment is done by default on the basis of element-type
The default setting may be changed with:
COLOR TYPE atom-type col (atom-type col ..)
Color is switched on/off with
COLOR (on/off)
or implicitly with
STRAW COLOR
This option may be combined with the 'Black-and-White' Patterns:
BWC (on/off)
Option 3:
Residues (i.e. unconnected species) can be displayed with differing colors with:
COLOR RESD
Option 4:
ARU's may be given distinguishing colors with instructions such as
ARU red 1555.01 1556.01
ARU green 1565.01
ARU-related colors are displayed with:
COLOR ARU (on/off)
or by clicking the 'col ARU' menu field
This option may be combined with the 'Black-and-White' Patterns:
BWC (on/off)
1.4.5.23 - Decoration Toggle
The boundary information (title, angles etc) may be switched (on/off) by clicking on
DECORATION.
1.4.5.24 - Graphics (META, POVRAY, RASMOL)
PLATON/PLUTON will generate by default an Encapsulated PostScript file of the image
displayed on the Image Canvas by clicking on the leftmost box button (indicated with
'EPS').
The Encapsulated PostScript default may be changed into HPGL with a code selection
button on the PLATON opening window, or with one of the keyboard instructions set meta
HPGL.
In the PLUTON mode, there are two interfaces available to other molecular graphics
programs.
- Clicking on 'Pov' will generate a file '.pov' suitable for the raytracing program POVRAY.
POVRAY will be executed when implemented.
- Clicking on 'Ras' will generate a 'PDB'structured '.ras' file suitable for the Molecular
Visualisation Program RASMOL. RASMOL will be executed when implemented.
The executables 'povray' and 'rasmol' are assumed to be globally accessible. Alternatively, a
path may be given in environment variables.
e.g. 'setenv POVEXE '/usr/local/bin/povray'
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