下载OLEX2或者Mercury等软件，打开*.cif文档，可以看到三维的分子结构。

Now, you will want to manipulate your structure modelto display a packing diagram, a fully-grown structure, or perhaps a few nearbymolecules to show close contacts. To do this, you will be working mostly withthe Symmetry Generation tab under the View menu. To follow along withthe commands below,start by clicking on the View button and then expand the “SymmetryGeneration” tab by clicking on it. You will see three sub-menus.

 

Symmetry Tools

This tool tab features a set of buttons for changingthe appearance/location of the asymmetric unit; expanding ("growing")a structure on the screen; viewing the basis vectors and unit cell; and othersimilar tasks.

 

Move Near

This is useful for moving moieties of a structureclose to a particular atom of interest.

1. Click on an atom near which another moiety is to bemoved.

2. Activate the mode by clicking on the Move Nearbutton (or typing 'mode move').

3. Click on an atom of each moiety that is to be movedclose to the initially selected atom.

 

Copy Near

This is a slightly different method for collectingmoieties of a structure close to a particular atom of interest.

1. Click on an atom near which another moiety is to becopied.

2. Activate the mode by clicking on the Copy Nearbutton (or typing 'mode move -c').

3. Click on an atom of each moiety that is to becopied close to the initially selected atom.

 

Assemble

Compaq: This command brings the various fragments of astructure as close together as possible on the screen.

Compaq –a: Brings fragments of a structure together asabove, but also assembles any "broken" fragments.

 

Growing

Olex2 shows the asymmetric unit by default. This tooltab contains very powerful techniques for "assembling" a structuremodel on the screen exactly as desired. It is then possible to refine the modelrepeatedly in Olex2 without dismantling this assembly.

 

Centre on Cell

All moieties outside the cell in the structure will becentred within the cell.

 

Centre on Largest Part

All moieties in the structure will be centred on thelargest moiety.

 

Show Basis

Displays/Hides thebasis vectors of this structure.

 

Show Cell

Displays/Hides theedges of the unit cell.

 

Quality

Use the slider tochange the quality of the display graphics from low (far left) to medium(middle) to high (far right). A lower quality setting may be useful if thecomputer struggles to display large structures.

Fuse

Display the asymmetric unit of the structure only. Allsymmetry-generated atoms will be removed. This is a command of fundamentalimportance.

 

Grow all

All symmetry-equivalent atoms required to show the"complete" structure will be displayed. In the case of polymericstructures, this is somewhat arbitrary, and more clearly defined 'grow'commands may need to be issued to display the structure as desired.

 

Packing

This tool tab provides methods of visualizing the 3Dpacking of a structure.

 

Growing

Growing here is used as a general term for addingatoms to the existing model on the screen in some systematic way, e.g., byadding symmetry-equivalent atoms to visualize an entire molecule when theasymmetric unit shows only part of the molecule because Z' < 1 for the structure.

 

Grow All

Generates all "missing" connectedsymmetry-equivalent atoms. This will usually suffice to expand an asymmetricunit to show a complete molecule.

 

Shells

This adds atoms in concentric shells outward from thestructure currently displayed on the screen.

 

Complete

Generates all missing symmetry-equivalent atoms of analready grown structure, whether bound to the main fragment or not. Thus, thiscommand will display symmetry-equivalent solvent molecules and counter-ions notgenerated by a plain 'grow' command.

 

Mode Growcommand

Similar to 'grow', but now the 'grow' command will beexecuted only when an object is clicked. Upon entering a growing mode, growable"bonds" will sprout from atoms satisfying the chosen growingconditions.

 

ShortContacts

Shows growable "bonds" to atoms involved in"short interactions" (e.g., hydrogen bonds) with the currentlydisplayed structure.

 

Van derWaals Radii

Shows growable "bonds" to other occurrencesof the currently selected atoms that are at most 2.0 Å away from the selectedatom.

 

Move

When a growable "bond" is clicked, thesymmetry-equivalent atom is moved to the new position. This is very useful whentrying to assemble a meaningful asymmetric unit for extended structures(polymers).

 

Shells

Shows growable "bonds" that can be clickedto grow the structure outward in concentric shells.

Assemble

Strictly speaking, this tool does not belong to theGrow family of tools, but it is frequently used together with the growingtools. It is used to rearrange components of the asymmetric unit for a morecompact or chemically sensible display of the model, often after a 'grow'operation.

 

Broken Fragments: 

Sometimes, parts of a model may become"broken" - parts that should be bonded are shown as separatefragments. This tool will bring them back together.

 

Atom-to-Atom: 

Similar to the Broken Fragments tool, but using adifferent reassembly algorithm.

 

Metal Last: 

In this tool, metal ions are first taken out of thereassembly process (which is very useful when trying to assemble a ligand!),after which they are placed at the shortest possible distance to the otheratoms in the structure.

 

Peaks: 

This moves all electron density peaks as close toexisting atoms as possible.

 

 

Packing

This tool tab provides methods of visualizing the 3Dpacking of a structure.

 

Expand Short Contacts

Use this slider bar to define the minimum distance forinteratomic "short contacts" such as hydrogen bonds or halogen bonds.As the slider moves to the right, more clickable "bonds" will beshown from atoms meeting the contact criterion. Alternatively, a number can beentered in the box next to the slider. Clicking on one of these"bonds" expands the display of the structure in the direction of thebond.

 

Pack Radius

Move the slider to the right to show allsymmetry-equivalent fragments around the current structure within the specifiedradius. It is also possible to type a number into the box adjacent to theslider.

 

Pack to limits

Displays all fragments of the structure within thelimits defined for unit cell edges a, b and c. The numbers in the box aremultiples of the edge lengths.

 

Fill Unit Cell

Displays only those atoms lying within the unit cell.

 

Complete Fragments

Completes any fragments that are only partiallydisplayed as a result of the various packing options. This is often usefulafter the Fill Unit Cell command.