addbonds
Adds a bond to the connectivity list
Selected
Selected Olex2 commands.
There are hundreds of commands in Olex2. This is a selection of those, that are most important for working with Olex2.
ads
Changes atom drawing style for all/selected atoms
afix
Refinement constraints
arad
Apply Radii to all/selected atoms
azoom
Changes the radii of all/given atoms
brad
Adjusts the bond radii in the display
calcfourier
Calculates Fourier map for current model.
calcvoid
Calculates Voids and Channels.
chiv
Chiral volume restraint
compaq
Move atoms and fragments together
conn
Maximum number of bonds
constrain
Generic macro to generate constraints
dang
Pairwise distance restraint
delbond
Remove a particular bond
delu
Rigid-bond APD restraint
dfix
Distance restraint
direction
Prints the current view direction
eadp
Equal ADP constraint
editatom
Brings up an edit window where the atom properties can be edited in ShelX format
editmaterial
Change properties of a graphical material
envi
Print the environment of a selected atom
exyz
Constrain atoms to the same site
file
Saves the current model to varios file formats
fix
Fix occupancy, xzy or Uiso
fixhl
Hydrogen atom names follow the parent atom
flat
Restrain all selected atoms to lie in a plane
free
Free occupancy, xyz or Uiso
fvar
Link parameters through a free variable
grad
Change the colour of the gradient background
grow
Grow atoms with various options
hklappend
Append reflections to the hkl file
hkledit
Opens dialogue listing ‘bad reflections’
hklexclude
Reversibly exclude some named reflections
hklstat
Prints detailed information about reflections
hklview
Show reflections in a reciprocal space view
htab
Search for hydrogen bonds and add them to the CIF
importfrag
Import a molecular fragment, with various options!
isor
Restrain the ADP towards being isotropic
kill
Delete atoms, bonds or labels
label
Add labels to atoms or bonds
load
Load a previously saved item.
lstsymm
List all symmetry operations for the current structure
match
A whole lot of tools for matching and overlaying things
matr
Orient the structure along cell axes
mode
A lot of things can happen when Olex2 is in a mode
mode fit
Fitting and splitting of fragments
mode fix u
Fixes Uiso or ADP for subsequently clicked atoms
mode fix xyz
Fixes the coordinates for subsequently clicked atoms
mode grow
Display directions where the molecule can grow… and then do a lot with that!
mode name
Naming mode. Powerful stuff!
mode occu
Sets the occupancy for subsequently clicked atoms
mode pack
Display the position of symmetry equivalent asymmetric units as tetrahedra
mode pack
Set to which PART the selected atoms will belong
mode split
Split or move atoms.
molinfo
Calculate molecular volumes and surface area for selected atoms
mpln
Find the best plane through the current selection
MSDSView
Displays the Mean Square Displacement options.
name
A bucket full of naming options
OFile
A portable version for making pictures
OFileDel
Delete the specified overlayed file
OFileSwap
Select the active file when overlay is on
omit
Omit reflections from the refinement. Either ranges, or explicitly named reflections.
pack
Pack the structure, with many different options
pict
Generate a bitmap image of the current structure
picta
Creates a POVRAY file of the current view
pictps
Make PostScript “ORTEP” style pictures
picts
Generate a stereo picture
pim
Helps with images where there are Metal-pi bonds
pipi
Analysis for pi-pi interactions
Reference
A list of the most commonly used Olex2 commands
restrain
Generic macro for restraint generation
rota
Rotate the molecule by a precice amount
rrings
Find and restrain rings
sadi
Apply the ‘same distance’ restraint
same
Set up a “same” system of restraints
save
Save things in Olex2 – various things!
scaleN
Extends the normal of one plane to touch another plane
sel
The most overloaded command in Olex2! You need to know about this…
sel atoms
Olex2 selection syntax concerning atoms
sel bonds
Olex2 selection syntax concerning bonds
sel bonds
Restrain a set of two bonds to be triangular with the provided parameters
selfont
Set the font used for various objects
sgen
Generate symmetry equivalent atoms
sgs
Space Group Settings
showp
Show only the named parts
simu
Apply a “similar ADP” restraint
sort
Sort the atom order in listings
split
Split the selected atoms into to parts
sump
Adding up occupancies to a fixed value
xf.rn.ShareADP1
Generate a shared, rotated ADP constraint
zoom
Get and Set the value of the current zoom level