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.

addbonds

Adds a bond to the connectivity list

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

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

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