current label unchanged.
3. Via sub-menu #2:
Click in the CONTENT MENU on RENAME ATOM, click on the atom to be
renamed and give new name via KEYBOARD options 1 or 2.
Note: It might be useful to click on 'Asym-Residue' to display the atoms in the asymmetric
unit only and/or select an individual residue (with Resd012) for large (many residue /
symmetry expanded) structures.
1.4.3.10 - MOVE LABEL
By default, PLUTON attempts to position labels at positions with no overlap of atoms,
bonds and other labels. This is generally fine for non-publication quality plots. Otherwise,
repositioning of labels will give an esthetically more pleasing presentation.
The MOVE LABEL toggle provides the tool to move a label to any desired position. Just
left button mouse click on the center of the label to be moved (The label will disappear).
Move the mouse cursor to the center of the new position and left mouse click again. This
operation can be repeated for all atoms (including the current one).
1.4.3.11 - CALC GEOM Toggle
The geometry around the clicked atom is displayed.
1.4.3.12 - ZOOM CENTER Toggle
Clicking on this option (turns RED) allows for the definition of a ZOOM centre by
clicking on a
particular atom of interest. Zooming is subsequently effected with the ZOOM option.
1.4.3.13 - ZOOM
The clicking in one of the ZOOM boxes allows zooming in to a particular environment in the
molecule. The zooming point is by default the centre of the plot unless redefined with the ZOOM
CENTER instruction.
1.4.3.14 – Select Residue(s) for Display
This button contains NRES (= number of residues) + 1 clickable boxes. By default, all
residues are shown. 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. Alternatively, residue #10 will be
displayed with the keyboard instruction
RESD 10.
1.4.3.15 - HFIX C-ATOM & ANISO
The
HFIX button gives access to a PLUTON facility to add H-atoms at calculated positions.
(Update of shelxl.res). See Section 1.3.2.15 for more details.
The
ANIS button gives access to a PLUTON facility to make atoms anisotropic (by clicking
). (Update of shelxl.res). See Section 1.3.7.8 for more details.
1.4.3.16 - VIEW OPTIONS
Clicking on one of the five pre-programmed boxes corresponds to the following instructions
and start orientations.
From left to right:
1. VIEW UNIT - Default orientation (XROT = 0, YROT = 0, ZROT = 0)
2. VIEW MIN - Minimum overlap orientation
3. VIEW XO - View down XO
4. VIEW YO - View down YO
5. VIEW ZO - View down ZO
1.4.3.17 – ATOM LABEL TOGGLE
Global atom labeling toggle. Clicking on the right box will also include H-atoms in the
labeling.
1.4.3.18 – Continuous Rotation About Y
Continuous rotation about y (= vertical/up) with speed corresponding to click position.
Continuous rotation about x (= horizontal) can be invoked with the instruction:
CROTX 0.1
Continuous rotation about z (= perpendicular) and in color can be invoked with the
instruction:
CROTZ COLOR 0.1.
1.4.3.19 - Stepwise Rotation About Z
Stepwise rotation about Z (perpendicular to image). Step size and direction based on click
position.
1.4.3.20 - Stepwise Rotation About Y
Stepwise rotation about the vertical (i.e. up) axis (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.
1.4.3.21 - Stepwise Rotation About X
Stepwise rotation about the horizontal axis (X). Clicking in the central area box gives small
rotation steps. Clicking further from the center corresponds to larger rotation steps.Clicking
left from the center or right from the center determines the sense of rotation.
1.4.3.22 - EXCLUDE ARU
Clickable ARU exclude
1.4.3.23 - OMIT OUTSIDE Toggle
Clicking on this button will force the display of the structure as far as it fits within the
crystallographic unit cell.
The effect of OMIT OUTSIDE is released by clicking on this button again.
1.4.3.24 – Asym-Residue Toggle
This toggle allows for switching of the display of molecules between the full list of active
ARU's and only those that make up the asymmetric unit. This feature can be useful in the
course of activities such as renaming atoms in multi-atom / multi-ARU cases.
1.4.3.25 - Reset & END Buttons
Clicking on RESET will make the program go back to a STICK style plot of the structure.
Return to the main PLATON menu by clicking on
END
1.4.4 – PLUTON SUB-MENU #2 (Style)
1.4.4.2 - SELECT PATTERN TOGGLE
This toggle activates a cycling option through the available 17 different black-and-white
patterns in response to clicks on atoms.
The menu option has two click positions:
1. Left Box: Change of pattern of all atoms of the same type as the clicked atom. (i.e.
clicking on O1 effects the pattern of all O).
2. Right Box: Change of all atom patterns simultaneously when clicked on one.(i.e.
clicking on O1 changes the pattern of all C,H,N etc.)
Subsequent clicks invokes cycling through the 17 available patterns.
See also the keyboard
BWC TYPE el bwc instruction (
Section 3.5.6)
1.4.4.3 - SELECT COLOR TOGGLE
With this toggle active (RED) colors may be changed per atom type by clicking on one atom
with the atom type to be changed. Subsequent clicking results in cycling through all
available color options.
The color loop involves:
- BLACK/WHITE
- RED
- GREEN
- BLUE
- YELLOW
- ORANGE
- VIOLET
- BROWN
