Changing the Model View

matr

[1,2,3 or abc] or [abc a1b1c1] or [x11 x12 x13 y11 y12 y13 z11 z12 z13]

Orients the model along a (1 or 100), b (2 or 010), c (3 or 001) or any other crystallographic direction, like 123, which sets current normal along (1*a+2*b+3*c) vector. Two crystallographic directions (from and to) may be specified align current view normal along the (to-from) vector. Also a full Cartesian matrix can be specified. If the directions are signed or consist of multiple digits all components should be of the same length like in 120101 or -1+1+1 (same as -10101). If no arguments given, prints current Cartesian orientation matrix.

Examples:

• matr 1 or matr a or matr 100 - sets current normal along the crystallographic a direction
• matr 100 011 sets current normal along (011-100) direction (the normal direction changes if from and to are swapped) 

rota

[axis angle] or [x y z angle increment]

Changes current view by rotating around given axis (x, y or z) when two arguments are provided and makes a continuous rotation around give axis when 5 arguments are provided. Note that X axis is aligned horizontally, Y - vertically and Z is out of the screen plane.

Examples:

• rota x 90 rotates the structure 90 degrees around X axis
• rota 0 0 1 90 1 rotates model in the screen plane (around Z) 90 degrees with 1 degree increment. 

direction

The command prints current normal in crystallographic coordinates and tries to match it to a crystallographic direction.

• -n sets the view along the normal of the plane
• -r: creates a regular plane

Keyboard Shortcuts

Ctrl+Q

ShowQ

Toggles between three states:

• show electron density peaks
• show electron density peaks with bonds
• hides electron density peaks

Ctrl+H

ShowH

Toggles between three states:

• show hydrogen atoms
• show hydrogens with internal h-bonds
• hides hydrogen atoms

Ctrl+T

ShowStr

Toggles between three states:

• show structure only
• show show structure and text
• show text only

Ctrl+I

sel -i

Inverts the current selection.

Ctrl+A

sel -a

Selects all atoms currently visible, however if labels are active (i.e. one or more label is selected) then this selects all labels.

Fixed/Refined Parameters

fix

{occu, xyz, Uiso} [atoms]

Fixes the specified refinement parameter, ie these parameters will not be refined in subsequent refinement cycles.

• occu: will fix the occupancy 
• xyz: will fix the xyz coordinates
• Uiso: will fix the whole ADP

• fix occu 0.5: will set and fix the occupancy of the current selection to 0.5
• fix xyz: will fix the x, y and z co-ordinates of the currently selected atoms, ie not refine them. 

free

{occu, xyz, Uiso} [atoms]

The opposite of fix - makes the specified parameters for the given atoms refineable. Feeing the occupancy is also available from the context menu.

mode

fixu

Fixes Uiso or ADP for subsequently clicked atoms.

mode

fixxyz

Fixes coordinates for subsequently clicked atoms.

mode

occu occupancy_to_set

Sets atoms occupancy to the povided value for subsequently clicked atoms.

Atom Connectivity Table Manipulation

conn

n [r] atoms

Sets the maximum number of bonds for the specified  atoms to n and changes the default bond radius for the given atom type to r.

Examples:

• conn 5 $C sets the maximum number of bonds all C atoms can have to 5,
• conn 1.3 $C changes the bonding radius for C atoms to 1.3 (the floating point is used to distinguish between n and r in this case!),
• conn 5 1.3 $C combines the two commands above

• -a: assembles broken fragments
• -c: similar to the default behaviour, but considers atom-to-atom distances and will move all atoms to the closest possible position to the largest fragment in the structure.
• -q: moves the electron density peaks close to the atoms.

addbond

A1 A2 or atoms

Adds a bond to the connectivity list for the specified atoms. This operation will also be successful if symmetry equivalent atoms are specified.

delbond

A1 A2 or Selected bond(s)

Removes selected bonds from the connectivity list.

• -s: by size
• -h: by heaviest atom
• -m: by molecular weight

• sort +m1 F2 F1 moiety +s will sort atoms by atomic mass and label, put F1 after F2 and form moieties sorted by size. Note that when sorting atoms, any subsequent sort type operates inside the groups created by the preceeding sort types.

Symmetry Operations

lstsymm

Prints symmetry operations and their codes for current structure.

envi

[r=2.7 Å] A1 or one selected atom [-h] [-q]

Note: if more than one atom is selected the first one is used

Prints a list of those atoms within a sphere of radius r around the specified atom.

• -h: adds hydrogen atoms to the list
• -q: option adds Q-peaks to the list

mode

grow [-s] [-v] [-b]

Displays the directions in which the molecule can be grown

• -s: also shows the short interaction directions
• -v: [2.0 Å] shows directions to the molecules within v value of the Van der Waals radii of the selected atoms which can be generated by clicking on the direction representations, only unique symmetry operations (producing shortest contacts are displayed)
• -r: shows directions to all symmetry equivalent atoms atoms of the selected one(s) within 15 Å
• shortcut Ctrl+g is used to enter the 'mode grow'

mode

pack

Displays the position of symmetry equivalent asymmetric units as tetrahedra. These asymmetric units can be generated by clicking on the corresponding tetrahedron.

sgen

atoms

The Symmetry operation is represented as 1_555, 1555 or -1+X,Y,Z and atoms as a selection or a names list

Generates symmetry equivalents of the provided (or all atoms, if there is no selection) using the provided symmetry operation.

Note: For symmetry operations starting with '-' and letter, a leading zero must be added, for example, 0-x,-y,-z, otherwise Olex2 confuses this with an option.

pack

a_from a_to b_from b_to c_from c_to [atoms]

Packs all or specified atoms within given dimensions

• -c: prevents clearing existing model

Example:  pack $O will pack all O atoms with the default of -1.5 to 1.5 cells range.

pack

cell

Shows content of the unit cell. In conjunction with 'grow -w' allows the creation of views where all asymmetric units contributing to the unit cell are shown.

pack

r

Packs fragments within radius r of the selected atom(s) or the centre of gravity of the asymmetric unit.

grow

[atoms] [-w]

Grows all possible/given atoms; for polymeric structures or structures that require to be grown several times Olex2 will continue grow until the operation results in a symmetry element that has been used previously.

• -w: permits the application of symmetry previously used operations to other fragments of the asymmetric unit

Example: If the main molecule is grown, but only one solvent molecule is shown, using 'grow -w' will produce other solvent molecules using symmetry operators used to grow the main molecule

Disorder Modelling: Constraints and Restraints

EXYZ

atom types (to add for the selected atom)
[-EADP]
[-lo]

Makes the selected site shared by atoms of several atom types.

• -EADP: adds the equivalent ADPs command for all atoms sharing one site.
• -lo: links the occupancy of the atoms sharing the site through a free variable.

EADP

atoms

Makes the ADP of the specified atoms equivalent.

SADI

atoms or bonds [esd=0.02]

For selected bonds or atom pairs SADI makes the distances specified by selecting bonds or atom pairs similar within the esd.

If only one atom is selected it is considered to belong to a regular molecule (like PF₆) and adds similarity restraints for P-F and F-F distances.

For three selected atoms (A1,A2,A3) it creates similarity restraint for A1-A2 and A2-A3 distances.

DFIX

d atom pairs or pairwise selection in order [esd=0.02]

For selected bonds or atom pairs DFIX will generate length fixing restraint with the given esd.

If only one atom is selected, all outgoing bonds of that atom will be fixed to the given length with provided esd. For three selected atoms (A1,A2,A3) the A1-A2 and A2-A3 restraints will be generated.

DANG

d atom pairs or pairwise selection in order  [esd=0.04]

For selected bonds or atom pairs, distance restraints similar to dfix will be generated.

tria

d1 d2 angle [esd=0.02]

For given set of bond pairs sharing an atom or atom triplets generates two dfix commands and one dang command.

Example: tria 1 1 180 C1 C2 C3 will generate 'DFIX 1 0.02 C1 C2  C2 C3' and 'DANG 2 0.04 C1 C3' it will calculate the distance for dang from d1 d2 and the angle.

FLAT

[atoms][esd=0.1]

Restrains given fragment to be flat (can be used on the grown structure) within given esd.

CHIV

[atoms][val=0] [esd=0.1]

Restrains the chiral volume of the provided group to be val within given esd

SIMU

[d=1.7] [esd12=0.04] [esd13=0.08]

Restrains the ADPs of all 1,2 and 1,3 pairs within the given atoms to be similar with the given esd.

DELU    

[esd12=0.01] [esd13=0.01]

'rigid bond' restraint

ISOR

[esd=0.1] [esd_terminal=0.2]

Restrains the ADP of the given atom(s) to be approximately isotropic

SAME

N

Splits the selected atoms into the N groups and applies the SAME restraint to them. Olex2 will manage the order of atoms within the in file, however mixing rigid group constraints and the 'same' instructions might lead to an erroneous instruction file.

split

[-r={eadp, isor, simu}]

Splits selected atom(s) along the longest ADP axis into two groups and links their occupancy through a free variable. 

• -r: adds specific restraints/constraints (EADP, ISOR or SIMU) for the generated atoms

AFIX

shelx afix number{mn}
[-n]

If no are atoms provided and afix corresponds to a fitted group where n is 6 or 9 (such as 106 or 79), all the rings which satisfy the given afix will be automatically made rigid (this is useful in the case of many PPh3 fragments); alternatively a single ring atom can be selected to make that ring rigid. In other cases, depending on afix either 5,6 or 10 atoms will be expected. Special cases of afix 0, 1 and 2 can be used to remove afix, fix all parameters or leave just the coordinates refinable, all other afix instructions will consider the first atom as a pivot atom and the rest - dependent atom.

• -n:  consider N-atoms as parts of rings

part

[part=new_part] [atoms]
[-p=1]

Changes part number for given/selected atom;

•  -lo: links occupancies of the atoms through a +/-variable or linear equation (SUMP) depending on the -p[=1]
• -p:   specifies how many parts to create. If -p=1, -lo is ignored and the given or new part is assigned to the provided atoms.

fvar

[value] [atoms]

This command links two or more atoms through a free variable.

• If no atoms are given the current free variables are printed.
• If no value is given but two atom names are give, the occupancies of those atoms are linked through a new free variable.
• If a value of 0 is given, the occupancy of the specified atoms will be refined freely
• if the value is not 0, the occupancy value of the specified atoms is set to the given value.

sump

[val=1] [esd=0.01]

Creates a new linear equation. If any of the selected atoms has refinable or fixed occupancy, a new variable is added with value 1/(number of given atoms), otherwise already used variable is used with weight of 1.0.

Example: If 3 atoms (A1, A2, A3) are selected this command will generate three free variables and insert the r2 1.0 var 3 instruction (equivalent to 1.0 = 1.0*occu(A1) + 1.0*occu(A2) + 1.0*occu(A3).

mode

split [-r={eadp, isor, simu}]

Splits subsequently clicked atoms into parts, or in combination with the Shift key can be used to drag an atom to change its position. While in the mode the newly generated atoms can be selected and moved as a group with Shift down or rotated when dragging the selection. The original and generated atoms will be placed into different parts.

• -r: can be used to generate extra restraints or constraints for original and generated atoms (see also the 'split' command); values EADP, ISOR or SIMU are allowed

Selection Syntax

sel

sel atoms where xatom.bai.mw > 20

Will select all atoms where the atomic mass is larger than 20

sel

Symmetry operation (represented by 1_555 or 1555)

Will select all currently shown symmetry generated atoms which were generated by the symmetry operation given.

HKL file Operations

hklstat

Prints detailed information about reflections used in the refinement.

Inserts 'OMIT h k l' instruction in the ins file

omit

val

Inserts 'OMIT h k l' for all reflections with  .

edithkl

[h k l]

Brings up a dialogue, where 'bad' reflections from the Shelx lst file and all its constituent symmetry equivalents can be inspected and flagged to be excluded from the refinement.

In constrast to the OMIT h k l instruction, which  excludes the reflection and all it equivalents, this dialogue allows to exclude those equivalents that are actually outliers.

If a particular reflection is specified, this particular reflection and all its constituent equivalents can be viewed.

excludehkl

-h=h1;h2;.. -k=k1;k2.. -l=l1;l2.. [-c]

This function provides a mechanism to reversibly exclude some reflections from refinement (these reflections will be moved to the end of the hkl file so they appear after the 0 0 0 reflection).

• -c: option controls how the given indices are treated, if not -c option is provided, then any reflection having any of the given h, k or l indices will be excluded, otherwise only reflections with indices within provided h, k and l will be excluded.

appendhkl

-h=h1;h2;.. -k=k1;k2.. -l=l1;l2..

Acts in the opposite way to excludehkl

For more advanced HKL processing, a Python script may be used. A sample hklf5.py script is provided in {Olex2 folder}/etc/scripts. The script can be copied and modified to accommodate any particular twinning law and run inside Olex2. The script allows creating an HKLF 5 file where reflections which belong to different twin components are assigned different batch numbers. To run a python script in Olex2 use the following command to load the script:

>>@py -l

This command shows a 'File Open' dialog, a python script can be selected. After loading the script can be modified and executed by pressing OK.

Customising the Olex2 GUI

setfont

{Console, Picture_labels} 

Brings up the dialog to choose font for the Console or Labels which end up on the picture. Built in function choosefont([olex2]) to choose system  or  specially prepared/portable font can be used to specify the font. 

• -p: a picture file name to be placed at the background 

• elp - represents atoms as ellipsoids (if ADP is available)
• sph - represents atoms as spheres
• ort - same as elp, but atoms have one of the quadrants cut out
• std - a standalone atom (i.e. grown as a cross in wire-frame mode)

• sfil - sphere packing radii (as in ShelXTL XP)
• pers - a fixed radii for model viewing
• isot - each atom has it's own radius depending on the value of the Uiso or ADP
• isoth - same as isot, but the H atoms are also displayed with their real Uiso's
• bond - all atoms get same radii as default bond radius
• vdw - the default/loaded Van der Waals radii used in most of the calculations

Output: Tables, Reports and Images

pictPS    

Generates a post-script file of what is visible in the molecule display.

• -atom_outline_color - the colour of the atom outline, used for extra 3D effect for the intersecting objects [0xFFFFFF]
• -atom_outline_oversize - the size of the outline [5]%
• -bond_outline_color - same as for the atom, can be changed to black to highlight bond boundaries 
• -bond_outline_oversize - the size of the outline [10]%
• -color_fill: Fills the ellipses with colour.
• -color_bond: Bonds will be in colour.
• -color_line: Lines representing the ellipses will be in colour.
• -div_pie: number [4] of stripes in the octant
• -lw_ellipse: line width [0.5] of the ellipse
• -lw_font: line width [1] for the vector font
• -lw_octant: line width [0.5] of the octant arcs
• -lw_pie: line width [0.5] of the octant stripes
• -p: perspective
• -scale_hb: scale for H-bonds [0.5]

pict

• ext {png, jpg, bmp}. png is best. 
• -pq: print quality

picta

• -pq: print quality
• -n: as for 'pict'

• -a: half of the view angle
• -s: separator width in %
• -h: the height of the output, by default equals to current screen height multiplied by the given resolution

label

• -type: {subscript, brackets, default}, the type only affects the PostScript labels and not applicable to the raster pictures

Structure Analysis

There are various tools available for the analysis of structures.

htab

• -g: if any of the rings is fully or partially constructued of symmetry generated atoms it grow the structure using those symmetry operators  

• -d: extra distance from the surface
• -p: precise calculation, each map voxel is tested, the default quick algorithm, uses the atom masks to find volume occupied by the molecule. The precise calculation is vectorised
• -r: resolution, a resolution of at least 0.1Å  and -p options is required to get values for publishing

• -g:  generation of the triangulation process
• -s: source of the triangles for the sphere triangulation, [o]ctahedron or [t]etrahedron are available

• -r: the resulting map resolution in angstrems
• -i: integrate the calculated map
• -scale: when Olex2 calculates structure factors, it uses the linear scale as a sum(Fo^2)/sum(Fc^2) by default, however a linear regression scale can be also used (use -scale=regression)
• -fcf: Olex2 will use an FCF with LIST 3 structure factors as a source of the structure factors. If this option is not specified, Olex2 will calculate the structure factors using the the reflection used in the refinement (use the 'hklstat' command to see more information on reflections).