3. 2 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.

CTRL+U sel -u Deselects all of current selection.

CTRL+G mode grow Enters mode grow. See also

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.

CTRL+U sel -u Deselects all of current selection.

CTRL+G mode grow Enters mode grow. See also symmetry operations.

CTRL+O reap Brings up the Open File dialogue.

F2 swapbg Swaps the background between white and coloured.

F3 labels Toggles labels on/off.

F4 grad -i Toggles gradient background on/off.

F5 Go to the work menu.

F6 Go to the view menu.

F7 Go to the tools menu.

F8 Go to the info menu.

F11 Fullscreen(true/false) Toggles full screen mode on/off.

Shift+F11 HtmlPanelVisible Toggles html panel on/off.

ESC

Exits current mode (some modes, like mode match, can

override this), clears current selection and text in the

command line

Break Interrupts the solution/refinement after the current cycle.

3. 3 Fixed/Refined Parameters

fix 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

Examples:

. 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 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.

{occu, xyz, Uiso} [atoms]

{occu, xyz, Uiso} [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.

labels -f show currently fixed atomic parameters, labels -f -r show labels for fixed atoms and also the

number at which the occupancy of riding atoms is fixed

3. 4 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

compaq [-a] [-c] [-q] Moves all atoms or fragments of the asymmetric unit as close

to each other as possible. If no options are provided, all

fragments are assembled around the largest one.

. -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.

sort [m] [l] [p] [h] atoms

[s] [h] [m] moiety

The sorting of atoms in the atom list is very powerful, but

also quite complex .

. -m: atomic weight

. -l: label, considering numbers





.

-p: part, 0 is first followed by all positive parts in

ascending order and then negative ones





.

-h: to treat hydrogen atoms independent of the pivot

atom.





Sorting of moieties



.

-s: by size



. -h: by heaviest atom

. -m: by molecular weight





Usage:



.

sort [+atom_sort_type] TBA

sort [Atoms] [moiety [+moiety_sort_type]



[moiety_atoms]] If just 'moiety' is provided -the atoms



will be split into the moieties without sorting.



Examples:



.

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.

Olex2 will display the altered connectivity table in the case if structure is grown or packed





3. 5 Symmetry Operations

lstsymm Prints symmetry operations and their codes for current

structure.

envi

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

[r=2.7 .] A1 or one selected

atom [-h] [-q]





.-v: [2.0 .] 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 .





.

shortcut CTRL+G is used to enter the 'mode grow'

Displays the position of symmetry equivalent asymmetric

units as tetrahedra. These asymmetric units can be generated

by clicking on the corresponding tetrahedron.



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.



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.



Equivalent to 'pack from to from to from to', like 'pack

0 1' is expanded to 'pack 0 1 0 1 0 1'



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.



Packs fragments within radius r of the selected atom(s) or

the centre of gravity of the asymmetric unit.



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





mode



sgen



pack



pack

pack



pack



grow



pack



atoms

The Symmetry operation is

represented as 1_555, 1555 or

-1+X,Y,Z and atoms as a

selection or a names list



a_from a_to b_from b_to

c_from c_to [atoms]



from to



cell



r





[atoms] [-w]





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





If some atoms are deleted after growing operations, Olex2 will use existing unique atoms as the asymmetric

unit atoms; this can be helpful to avoid a sequence of sgen/kill commands.

labels -l -i: Adds labels only to the 'original' - i.e. not created by symmetry - molecule.





In a packed structure: Right-click on a bond > Graphics > Select the Groups(s): Will select all bonds

(or atoms) of that type in the grown structure.

3. 6 Disorder Modelling: Constraints and Restraints

EXYZ

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 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.

atom types (to add for the

d atom pairs or pairwise

selection in order [esd=0.02]





d atom pairs or pairwise

selection in order [esd=0.04]

DANG 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.

showp [any]; space separated part

number(s)

Shows only the parts requested: showp 0 1 will show parts 0

and 1, showp 0 just part 0. showp by itself will display all

parts.

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



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.





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.

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).



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





part [part=new_part] [atoms]

[-p=1]



fvar



[value] [atoms]

sump [val=1] [esd=0.01]



mode

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









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

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

3. 7 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.

sel sel rings NC5 Will select all NC5 rings in the structure

sel sel part 1 Will select part 1 of the structure

3. 8 HKL file Operations

hklstat Prints detailed information about reflections used in the

refinement.

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

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

omit s 2theta Inserts 'OMIT s 2theta' instruction in the ins file

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]



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





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.



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.



3. 9 Customising the Olex2 GUI

setfont {Console, Picture_labels}



grad [C1 C2 C3 C4]

[-p]



r [hbonds]



brad operates on all or selected

bonds



ads {elp, sph, ort, std}





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.



Choose the colour of the four corners of the graduated

background.



.

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



Adjust the bond radii in the display. If the 'hbonds' is

provided the second argument, the given radius is applied to

all hydrogen bonds.



A function for drawing styles development. Changes atom



draw style for all/selected atoms.



.

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









{sfil, pers, isot, isoth, bond,



arad



vdw}



azoom



% [atoms]





3. 10 Output: Tables, Reports and Images

pictPS filename.ps 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]

The bond width is taken from the display. This can be

changed with brad

pict filename.ext [n=2]

[-pq]

Generates a bitmap image of what is visible on the molecule

display. n Refers to the size of the output image. If n is

smaller than 10, it refers to a multiple of the current display

.

std - a standalone atom (i.e. grown as a cross in wire-

frame mode)

A function for drawing styles development; applies different

radii to all/selected atoms.



.

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

Changes the radii of all/given atoms, the change is given in



percents.









filename.ext [n=1]

[-pq]



picta



filename.ext [n=1]

[-a=6]



picts



[-s=10]

[-h=n*(screen height)]





label [atoms]



label





size, if it is larger than 100, it refers to the width of the image

in pixels.



. ext {png, jpg, bmp}. png is best.

.-pq: print quality

A portable version of pict with limited resolution (see

explanation for n above), which is OS and graphics card

dependent. This may not be stable on some graphics cards



.

-pq: print quality



.

-n: as for 'pict'



Creates a 'stereo' picture with two views taken with the +/





a option rotation around y axis and placed onto one picture



separated by s pixels.



.

-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



Adds labels to the selected atoms. These labels can be moved

by pressing the SHIFT key while holding down the left mouse

button



.

-type: {subscript, brackets, default}, the type only affects

the PostScript labels and not applicable to the raster

pictures，

3. 11 Structure Analysis

There are various tools available for the analysis of structures.



[minimal angle=150°]

[maximum bond length 2.9 .]

[-t]

[-g]





htab



pipi



[centroid-to-centroid distance

4 .]

[centroid-to-centroid shift 3 .]

[-g]







Searches and adds found hydrogen bonds (like HTAB and

RTAB in Shelx) into the list for the refinement program to

add to the CIF. Equivalent symmetry positions are

automatically inserted and merged with the existing ones.

The command can be executed several times with different

parameter values, only one unique instructions will be

added.



.

-t: adds extra elements (comma separated like in -t=Br,I)

to the donor list. Defaults are [N,O,F,Cl,S]



.-g: if any of the found bonds are generated by symmetry

transformations, the structure is grown using those

symmetry transformation



The command analyses the p-p interactions (only stacking

interactions for now) for flat regular C6 or NC5 rings and

prints information for the ones where the intercentroid









distance is smaller than [4] . and the intercentroid shift is



smaller than [3] ..



.

-g: if any of the rings is fully or partially constructued of

symmetry generated atoms it grow the structure using

those symmetry operators



Calculates and displays the structure map. Also calculates the

largest channels along crystallographic directions and the



packing index.



.

-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 0.1. and -p options

is required to get values for publishing



Note:



The radii used in the calculation are currently coming from

the CSD website:

http://www.ccdc.cam.ac.uk/products/csd/radii

However there are several ways how the radii can be

changed, one of the ways is to provide a file name with radii

([element radius] a line format), the other one is to load the

radii from the same kind of the file using 'load radii vdw'

command.



Calculates molecular volume and the surface area for all/



selected atoms.

. -g: generation of the triangulation process

. -s: source of the triangles for the sphere triangulation,



[o]ctahedron or [t]etrahedron are available



Generation 5 for octahedron approximate sphere by 8192



triangles, for tetrahedron by 4096 triangles, each generation



up increases the number of triangles by factor of 4,

generation down - decreases it by the same factor.



Calculates Fourier for current model



.

-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).



Calculates and displays Patterson map





calcvoid



molinfo



calcfourier



calcpatt



[radii file name]

[all atoms/selected atoms]

[-d=0]

[-p]

[-r=0.2.]





[radii file name]

[atoms]

[-g=5]

[-s=o]





{-calc,-diff, -obs, -tomc}

[-r=0.25.]

[-i]

[-scale=simple]

[-fcf]





Notes etc about Structure Analysis









4. Appendix

4. 1 About Versions and Tags

The Olex2 distribution system has undergone many changes since the project was started in

2004. We have always aimed at providing program updates as soon as possible to the Olex2 user

community. We think that one of the best ways to encourage bug reports and suggestions is to

translate this user feedback as soon as possible into real improvements in the software.



For a while -up to about December 2009 -we have made updates available on a very frequent

basis. This has met with a warm welcome from many of our users, but has also caused some

problems: Not all updates did only do what they were supposed to do! At that point, we have

decided to change the policy somewhat, and have come up with the following system for the

distribution of Olex2.



There are now distinct versions of Olex2. Before Version 1.0, everything consisted of

continuously updated files. At some point, this became no longer supportable, and we decided

to introduce proper versions into the Olex2 distribution system. Any new version requires a

complete re-install. However different versions of Olex2 can exist next to each other without

causing any interference. For each version of Olex2, there are three 'tags', referring to different

source repositories. For example, for Version 1.1 there are the following tags:



. 1.1-alpha

. 1.1-beta

. 1.1

Alpha: Whenever we made some changes, we 'make' an alpha distribution of Olex2. We use

this version for in-house testing (although you are very welcome to use this version too, as long as

you are aware of the fact that this version is typically very experimental and will very likely cause

some problems. However, if you have suggested a new feature, or reported a bug fix, you may well

find that we have implemented your suggestions already!



Beta: Once we've done some testing of this alpha version, we 'promote' it to the beta

distribution. This version is tested by a wider group of testers -these tend to be those users with

whom we have a lot of contact.







Release: Once a distribution has been tested in the beta stage, a proper release is made. This

can be expected to be stable and if you encounter any problems with release version, please tell

us about this! It doesn't matter how small the problem is, we'd like to know.



4. 2 Installing Olex2

4. 2. 1 Windows:

.

Please download the Olex2 installer from the Windows tab and run it. Select the

destination folder to which to install Olex2 (typically C:\Program Files\Olex2). If you

do not have administrator privileges, please select a folder where you have full access

rights.

.

Make sure you select the latest version of Olex2—Version 1.1—from the download

repository.

.

Click on Install. This will install Olex2 on your computer. When it is done, there will be

a ‘Run’ button on the installer form. Click this to run Olex2. The first time Olex2 runs on

your computer, it will take some time to start up (up to one minute!).

Olex2 should now be opened, there should be no red (error) lines in the main window

and there should be a molecule of sucrose displayed on the screen. Olex2 does not require

any third party programs to perform structure analyses—Structure Solution as well as Structure

Refinement—but, if you have a ShelX licence, you may want to make sure that Olex2 can interact

with the ShelXS, ShelXL and ShelXM. If you do not have a ShelX licence, and would like to obtain

one, please go to the ShelX Pages for more information.



Please note that the ShelX executables that are shipped with WinGX do not work with Olex2.



You can either copy your ShelX executables into the Olex2 installation folder, or—better—you

can copy your executables into a folder which you then add to the PATH variable of Windows.

For example, create a folder C:\Program Filex\Shelx, then Right-Click on ‘My Computer’ (XP)

or ‘Computer’ (Vista and 7) and select Properties. Then select Advanced. There you can add the

location of your ShelX executables to the PATH variable.



4. 3 External Programs

4. 3. 2 SHELX

All programs of the SHELX family can interact seamlessly with Olex2. There is no need for

registering any of these programs with Olex2, it is enough if the folder containing the ShelX

programs are on the system PATH. This is normally the case if ShelXTL has been installed on a

system. Otherwise, you will need to set you system PATH variable to include the folder where you

keep your SHELX executables.







Please note that the SHELX executables that are shipped with WinGX do not work with

Olex2. These executables have been modified in such a way that they will only work properly with

WinGX. Since WinGX puts the folder that contains these executables on the system PATH, you

might find that SHELX appears in Olex2 -and then doesn't work. In this case, you will need to get

new SHELX executables and put them in the same folder where Olex2 is installed -executables

found there will be used by Olex2 preferentially.



4. 3. 3 Platon

John Warren has provided an interface to PLATON.



4. 3. 4 SuperFlip

Arie van der Lee has provided an interface to SuperFlip.



4. 4 About Macros and Scripting in Olex2

Olex2 supports two different tpes of external scripting: Macros and Python scripts.

为何不能作为附件发出来？

不会弄附件

可以发一下该软件么

我怎么没有在这个软件中找到哪个部分能代替shelxtl中的xprep的功能，也就是说，我只有p4p 文件和raw文件不知道怎么定空间群。