Index
Numerics -
A -
B -
C -
D -
E -
F -
G -
H -
I -
J -
L -
M -
N -
O -
P -
R -
S -
T -
U -
V -
W -
X -
Y -
Z -
Symbols
Numerics
90 degree rotation
A
a axis
definition
viewing along 1 2
a* axis
definition
viewing along
Actual distance, in defining contacts
Adding
bonds to structures
Adding hydrogens
to structures, automatically
to structures, manually
ADP type, viewing in spreadsheet
Ambient lighting, controlling
Analogues
Angle picking mode
Angles, measuring
Anorthic
Arrows in tool bar
Asymmetric unit 1 2
Atom colours
by element
by symmetry equivalence
customised
global (all atoms)
setting for individual atoms
Atom labels
description
global (all atoms)
hydrogens
non-hydrogens
show/hide all labels
show/hide specific labels
toggling on and off
Atom selection
deselecting
selecting
yellow dots on selected
Atom styles
ball and stick
capped stick
global (all atoms)
setting for individual atoms and bonds
show/hide atoms
spacefill
wireframe
Atomic coordinates
fractional
output of
reading in
Atomic displacement parameters
Atomic Displacement Parameters (ADP) display style
description
displaying
setting display options
Atomic vibrational parameters
Authors
Auto editing options
add missing hydrogens
guess bond types
standardise to CSD bond type conventions
Average sigma (C-C)
Axes, crystallographic
colouring conventions
description
displaying
reciprocal
viewing along
B
b axis
definition
viewing along
b* axis
definition
viewing along
Background
left-clicking in
right-clicking in
Background colours, setting
Ball and stick display style
BFDH theoretical crystal morphology
displaying
setting display options
Bioactivity
Bitmap (*bmp) file images
Blue contacts (non-hanging)
bmp files
Bond styles
ball and stick
capped stick
global (all bonds)
setting for individual
spacefill
wireframe
Bond type conventions
standardising
Bond type display conventions
Bond types
guessing
setting
standardising to CSD conventions
Boundary planes of slices
Bravais, Friedel, Donnay and Harker (BFDH) theoretical crystal morphology
displaying
setting display options
Browsing
Cambridge Structural Database
hits from ConQuest search
other CSD-format databases
Build Network (page in Contacts dialogue box)
Building
network of contacts
packing diagram
C
c axis
definition
viewing along
c* axis
definition
viewing along
Calculate, top-level menu button
Cambridge Structural Database
browsing complete CSD
description
viewing additional information
viewing ConQuest hits
Capped stick display style
cde style, command line option
Cell angles
Cell lengths
Cell parameters, explanation
Cell volume
Centroids
colouring
creating
deleting
displaying
labelling
opacity
show/hide centroids
transparency
use in measurments
cif files
description
reading
saving
cif format
Clearing measurements
client, command line option
Clipboard, copying to
Colour
background, setting
Colouring
atoms, globally
atoms, individually
bonds, globally
bonds, individually
by element type
by symmetry equivalence
centroids
customising
globally
planes
Select color dialogue box
Colouring conventions
cell axes
elements
nonbonded contacts
selected atoms
Command line options
Compound name
Conformer
ConQuest, CSD search program
description
transferring search hits to Mercury
Contacts, nonbonded
basic steps in defining and displaying
blue
building a network
colouring conventions
copying definitions
cyan
default definitions
defining new types of 1 2
deleting definitions
displaying
distance limits
editing definitions
hanging
hydrogen bonds, customised
hydrogen bonds, default
intramolecular
list of
networks
overview
red
short nonbonded contacts
specific nonbonded contacts
switching on and off
Coordinates
fractional, explanation
Coordinates, atomic
fractional
output of
reading in
Copy
Crystal chemical unit
colouring
displaying
Crystal face
displaying
Crystal packing
one unit cell
setting packing ranges
several unit cells
slices through crystals
switching on and off
Crystal system
Crystallographic axes
colouring conventions
description
displaying
reciprocal
viewing along
Cubic
Customised
colours
nonbonded contact definitions
powder pattern display settings
spreadsheet data items
Cyan contacts (non-hanging)
D
Databases, top-level menu button
adding databases to
viewing different databases
Default
element colours
hydrogen-bond definition
short nonbonded contact definition
view direction
Deleting
atom labels, all
atom labels, specific
centroids
contacts in network
hanging contacts
hydrogen bonds, definitions of
hydrogen bonds, from display
measurements
molecules from network
nonbonded contacts, definitions of
nonbonded contacts, from display
planes
Density
Depth cueing, setting
Deselection of atoms and molecules
Dial box
flipping by 90 degrees
rotation
scaling
translation
Dialogue Boxes
Atom Colours
Atom Labels
Atom Styles
Centroids
Contacts (Build Network page)
Contacts (Find Contacts page)
Define H-bonds
Define Short Contacts
Define Specific Contacts
Packing and Slicing
Plane Properties (Atoms page)
Plane Properties (hkl page)
Save Image
Select color
Show/hide Atoms
Diffraction details
directrendering, command line option
Disordered structures
Displacement entry box
Display
additional information about structure
ADP type in spreadsheet
ADPs
area in interface
atoms and their properties in spreadsheet
BFDH crystal morphology
bonds and their properties in spreadsheet
button in top level menu
centroids
chemical diagram in spreadsheet
contacts and their properties in spreadsheet 1 2 3 4
copying to clipboard
flipping view direction
geometry
hydrogen bonds
left clicking (picking)
networks
nonbonded contacts
packing
perspective
planes
resetting default perspective
resetting default scale
resetting default view
right-clicking in
rotating
saving image as file
scaling
slices through crystals
spreadsheets
text information in spreadsheet
top-level menu button
translating
Uequiv values in spreadsheet
Uij values in spreadsheet
unit cell axes
unit cell contents
view along crystal axes
view along planes
view perpendicular to planes
zooming
Display defaults, resetting
Display properties
ADPs
atom colours, setting globally
atom colours, setting individually
atom labels, setting globally
atom labels, setting individually
atom styles, setting globally
atom styles, setting individually
ball and stick
bond colours, setting globally
bond colours, setting individually
bond styles, setting globally
bond styles, setting individually
capped stick
show/hide
spacefill
wireframe
Displaying
multiple structures simultaneously
Displaying individual structures
Distance
hydrogen bond
limits for nonbonded contacts
measuring
Distance picking mode
Donors, in hydrogen bonds
Drag and drop
E
Edit, top-level menu button
Copy
Deselect All
Invert Selection
Redo
Select All
Undo
Editing
centroid display properties
distance limits for nonbonded contacts
hydrogen-bond definitions
nonbonded contact definitions
packing ranges
plane display properties
Editing structures
adding bonds
adding hydrogens
removing atoms and bonds
removing molecules
setting bond types
Element colours
Ellipsoid display
options
style
Entry ID (refcode)
Environment variable, for databases
Expand Contacts picking mode
Expansion of networks
explanation of
methods
Experimental notes
Exporting
images as .bmp files
images as .png files
images to clipboard
structures, external formats
structures, Mercury (.mry) format
F
Face, of crystal
displaying
File, top-level menu button
Open
Save As
filename, command line option
Find Contacts (page in Contacts dialogue box)
Flipping view direction
Formula
Fractional coordinates
explanation of
G
Geometry, measuring
angles
clearing from display
distances
torsions
Graphics window operations
flipping view direction
perspective
resetting default perspective
resetting default scale
resetting default view
rotating
scaling
translating
view along crystal axes
view along planes
view perpendicular to planes
Greying out
Guess bond types
H
H-Bond Default definition
Habit
Hanging contacts
colouring conventions
explanation
generating
in network expansion
Hexagonal
Hiding
atom labels, all
atom labels, specific
atoms
bonds
centroids
hydrogen atoms
hydrogen bonds
measurements
molecules
nonbonded contacts
planes
hkl (Miller) planes
colouring
creating
deleting
displaying
labelling
opacity
show/hide
slices through crystals
transparency
viewing along or perpendicular to
Hue (of colour)
Hydrogen atoms
adding to structures, automatically
adding to structures, manually
hiding
imprecision in X-ray structures
labelling all
missing
use of, in defining hydrogen bonds
Hydrogen bond
acceptors
angle
basic steps in defining and displaying
building a network
colouring conventions
contacts list
copying definitions
default definition
defining new types of
deleting definitions
dialogue box
displaying
distance limits
donors
editing definitions
hydrogen atom positions, use of
intramolecular
list of
overview
switching on and off
viewing definitions
I
Identifier
Images
copying to clipboard
flipping view direction
perspective
resetting default perspective
resetting default scale
resetting default view
rotating
saving as file
scaling
translating
view along crystal axes
view along planes
view perpendicular to planes
zooming
Importing
databases
results of ConQuest search
structures in external formats
Increment
for controlling rotate speed
for controlling translate speed
for controlling zoom speed
Input
of ConQuest search results
of databases
of structures in external formats
Interface, overview
Intramolecular contacts
J
jpeg files
jpg files
L
Label (picking mode)
Labelling
atoms, all
atoms, specific
centroids
hydrogens, all
non-hydrogens, all
planes
Least-squares mean planes
colouring
creating
deleting
displaying
labelling
opacity
show/hide
slices through crystals
transparency
viewing along or perpendicular to
Least-squares overlay of structures
Left clicking in display
Lighting effects, setting
Lightness (of colour)
Limits
distance, in contact definitions
of slice through crystal
Literature reference
Loading
databases
results of ConQuest search
structures in external formats
M
Maximum distance +/- entry box
Measurement
angles
clearing from display
distances
torsions
Measurment
involving centroids
involving planes
Melting point
Mercury (.mry) files
reading
saving as
Middle mouse button
Miller planes
colouring
creating
deleting
displaying
labelling
opacity
show/hide
slices through crystals
transparency
viewing along or perpendicular to
Missing hydrogen atoms
Modify, top-level menu button
Auto edit structure
Edit structure
mol files
description
reading
mol2 files
description
reading
saving
Molecular networks
basic steps in building
colouring conventions
deleting contacts from
deleting molecules from
dialogue box
hanging contacts
network expansion, methods
network expansion, overview
nonbonded contacts
overview
resetting a network
Molecule
Molecules
ball and stick
capped stick
colour by element type
colour by symmetry equivalence
colours, setting globally
colours, setting individual
deselecting
selecting
show/hide molecule
spacefill
toggling molecules on/off
wireframe
Monoclinic
Morphology, BFDH
motif style, command line option
motifplus style, command line option
Mouse buttons
for changing perspective
for changing scale
for rotating
for translating
left clicking
right clicking
mry files
reading
saving as
N
Networks of contacts
basic steps in building
colouring conventions
deleting contacts from
deleting molecules from
dialogue box
expansion, explanation of
expansion, methods
hanging contacts
nonbonded contacts
overview
resetting a network
nodirectrendering, command line option
Non-hydrogen atoms, setting display properties
Non-positive-definite atoms, display options (in ADP display mode) in Mercury
Nonbonded contacts
basic steps in defining and displaying
building a network
colouring conventions
copying definitions
default definitions
defining new types of
deleting definitions
displaying
distance limits
editing definitions
hydrogen bonds, customised
hydrogen bonds, default
intramolecular
list of
networks
overview
short nonbonded contacts
specific nonbonded contacts
switching on and off
viewing definitions
Normals to planes, viewing along
O
Opaque, setting planes or centroids to be
Ortho-flip of display
Orthorhombic
Orthorhombic crystal system
explanation
Other cell details
Output
images as .bmp files
images as .png files
images to clipboard
structures, external formats
structures, Mercury (.mry) format
Overlaying structures
Overview
atom and molecule display
centroids and planes
colouring conventions
crystal packing
interface
networks
nonbonded contacts
reading files
saving files
slices through crystals
P
Packing diagrams
one unit cell
packing ranges
several unit cells
slices through crystals
switching on and off
Packing ranges
pdb files
description
reading
saving
pdb format
Peptide sequence
perspective, display
changing
resetting to default
Phas transitions
Picking modes
Angle mode
Distance mode
Expand Contacts mode
Select mode
Torsion mode
Pixels, number of, in saved images
Planes
boundary, of slices
colouring
creating least-squares
creating Miller
deleting
displaying
labelling
Miller, definition
opacity
show/hide
slices through crystals
transparency
use in measurments
viewing along or perpendicular to
platinum style, command line option
png files
Polymorph
portable network graphics (png) file
Powder diffraction pattern
customised settings
displaying
Full Width at Half Maximum value, setting
saving
technical details
Powder study
PreQuest
viewing databases created by
Pressure
Protons
imprecision in X-ray structures
missing
undisplaying
use of, in defining hydrogen bonds
R
Radiation probe
Radiation source
Range
distance, in contact definitions
packing
Reading
databases
results of ConQuest search
structures in external formats
Real cell axes
colouring conventions
description
displaying
viewing along
Reciprocal cell axes
definition
viewing along
Recrystallisation solvent
Red contacts (hanging)
Red, green, blue colour values
Redoing commands
Refcode
definition
list of, in main window
Refinement details
Remarks
Removing
atom labels, all
atom labels, specific
centroids
contacts in network
hanging contacts
hydrogen bonds, definitions of
hydrogen bonds, from display
measurements
molecules in network
nonbonded contacts, definitions of
nonbonded contacts, from display
planes
Removing atoms and bonds from structures
Require H-atom positions known
res files
description
reading
saving
res format
Resetting to default display
rgb colours
Rhombohedral
Right-clicking in display
Rotating display contents
by 90 degrees
S
Saturation (of colour)
Saving
images as .bmp files
images as .png files
Images as jpeg or jpg files
images to clipboard
powder pattern (.xye) format
structures, external formats
structures, Mercury (.mry) format
Saving spreadsheets
csv format
tsv format
txt format
Saving structures
cif format
Mercury format
mol2 format
pdb format
res format
Scaling the display
sd files
description
reading
Search of CSD, viewing hits from
Sections through crystals
boundary planes
creating
displacing
Select picking mode
Selection
of atoms and molecules
of structures for viewing
top-level menu button
Sensitivity
Separated by, intramolecular contacts option
Setting
background colours
depth cueing
lighting effects
sgi style, command line option
Short Contact, less than (sum of vdw radii)
Short nonbonded contacts
basic steps
building a network
colouring conventions
copying definitions
default definition
defining new types of
deleting definitions
dialogue box
displaying
distance limits
editing definitions
intramolecular
list of
overview
switching on and off
viewing definitions
Showing/hiding
atom labels, all
atom labels, specific
atoms
bonds
centroids
hydrogen atoms
hydrogen bonds
molecules
nonbonded contacts
planes
Sign, of torsion angle
Slabs of crystals
Slices through crystals
boundary planes
creating
displacing
Source
Space group
Specific nonbonded contacts
basic steps
building a network
colouring conventions
copying definitions
defining new types of
deleting definitions
dialogue box
displaying
distance limits
editing definitions
intramolecular
list of
overview
switching on and off
viewing definitions
Speed
of rotation
of translation
of zooming
Spreadsheets
atoms and their properties, display of
bonds and their properties, display of
chemical diagram, display of
contacts and their properties, display of 1 2 3 4
data items, availability of
data items, customising display of
manipulating
saving
textual information, display of
Standardising bond types
Status bar
Structures, editing in Mercury
adding bonds
adding hydrogens
removing atoms and bonds
removing molecules
setting bond types
Structures, viewing in Mercury
Cambridge Structural Database
CSD-format databases
from ConQuest search
from external format files
individual structures
multiple structures simultaneously
Style, box in main Mercury window
style, command-line option
Supressed atoms
Sybyl atom type
Synonym
T
Temperature
Temperature factor 1 2
Tetragonal
thermal ellipsoids
Tool bar
use for rotating display
use for translating display
use for zooming display
Top-level menu
Torsion (picking mode)
Torsion angles
definition
measuring
Translating display contents
Transparent, setting planes or centroids to be
Triclinic
Trigonal
Type, bond
setting for structures
U
Uequiv values, viewing in spreadsheet
Uij values, viewing in spreadsheet
Undisplaying
atom labels, all
atom labels, specific
atoms
bonds
centroids
hydrogen atoms
hydrogen bonds
measurements
molecules
nonbonded contacts
planes
Undoing commands
Unit Cell
colouring conventions for axes
definition
displaying axes
displaying contents of many
displaying contents of single
labelling axes
packing ranges
reciprocal axes
slices through
switching packing on and off
viewing along axes
Unit Cell Parameters, explanation
V
van der Waals radii
default values of
in distance limits for contacts
Viewing
along plane
along reciprocal cell axes
along unit cell axes
individual structures
multiple structures simultaneously
perpendicular to plane
W
windows style, command line option
Wireframe display style
X
x rotation
x-90, x+90
xye files
description
saving
xye format
Y
y rotation
y-90, y+90
Yellow dots on atoms
Z
z rotation
z-90, z+90
Zooming the display
Symbols
-client, command line option
-directrendering, command line option
-nodirectrendering, command line option
-style, command line option
