Geometric Analysis of Structures

Get (bond) distances and angles, π-π interactions, overlays etc

Overlaying Structures

It is frequently useful to be able to overlay structures either to compare the orientation of common fragments in the same structure (e.g. when Z'>1) or between two different structures (e.g. a different polymorph, structures before and after a phase transition or spin-crossover). Overlaying the structures makes it much simpler to identify differences.

Before trying to overlay structures delete all Q-peaks, e.g. type >>kill $Q.

Automatically overlaying fragments in the same structure

In situations where there are two fragments in the structure with the same connectivity, under Tools|Overlay click on Match All Fragments. Olex2 will overlay the structures on the screen and calculate a root mean square distance (RMSD) deviation for overlay of the fragments. This is displayed on the graphics screen with and without inversion or alternatively type >>match. To return to unmatched fragments click on UnMatch or type >>fuse.

The automatic matching does not always work if there is disorder in a molecule (try matching selected atoms) or if it is of high symmetry. In the case of a high symmetry example, try hiding hydrogen atoms (Ctrl+H) or manually change an atom type to break the symmetry. This is because the graph matching algorithm does not use pattern recognition for the optimisation and high symmetry can introduce a large number of possible permutations, e.g. a –CH\low{3} group increases the number of permutations by 6.

Matching selected atoms in the same structure

If the automatic matching did not work or different atoms are required to be matched, it is possible to match selected atoms.

Select 3 atoms in the first fragment and then 3 atoms in the second fragment in the order to be matched. Under Tools|Overlay select Match Selected Atoms. To return to the unmatched structure, click on UnMatch or type >>fuse.

Tools|Overlay|Mode-Match This mode enables interactive matching by a maximum of three pairs of atoms. The first pair of atoms are superimposed, the second pair causes a rotation to minimize the distance between the atoms of the second pair, the third pair causes rotation around the line formed by the first and second pair to minimize the difference between the atoms of the third pair. Hit ESC to exit this mode. To return to the unmatched structures click on UnMatch or type >>fuse.

Overlaying molecules from different structures

Click on Tools|Overlay|Overlay-Structure to overlay a second structure. The two structures now appear on the right and left hand side of the graphics screen and the user-selected matching mode is automatically set up. A maximum of three pairs of atoms from the two structures can be selected.

To remove the overlaid structure, select Remove Overlay from Tools|Overlay. Alternatively, after clicking on Tools|Overlay|Overlay Structure, press ESC.

Calculating Geometric Parameters

Measuring bond distances

  • Hovering over a bond with the mouse will display the bond length of that particular bond.
  • RIGHT CLICK on the bond and the bond length will be displayed at the top.
  • Select two atoms, then under View|Geometry click on either Distance and Angles (of selection) or Distance and Angles with esd (of selection) to obtain the distance with or without an esd (the latter always requires the use of View|Geometry Refine and save esd info first.)
  • Right click over an atom, under BANG is a list of all bond lengths or distances to nearby Q-peaks.
  • Select one/two atoms and type >>bang to see associated geometric parameters (you can also supply atom names).
  • Under Work click on Report to generate an html report containing the bond lengths in one of the tables.

Measuring bond angles

  • RIGHT CLICK on the central atom, under BANG the bond angle will be displayed.
  • Select three atoms, then, once again, under View|Geometry click on either Distance and Angles (of selection) or Distance and Angles with esd (of selection) to obtain the distance with or without an esd.
  • Select the central atom and type >>ang sel to see associated geometric parameters (alternatively replace sel by an atom name).
  • Select Work|Report to generate an html report containing the bond lengths in one of the tables.

Measuring torsion angles

  • RIGHT CLICK on the central bond, under TANG any torsion angles associated with the bond will be displayed.

  • Select four atoms, then, once again, under View|Geometry click on either Distance and Angles (of selection) or Distance and Angles with esd (of selection) to obtain the distance with or without an esd respectively.

  • To tabulate the torsion angles:

    • Click on the pencil icon to open the .ins file header.
    • Type >>CONF on a separate line somewhere below the UNIT line and Refine.
    • Select Work|Report to generate an html report containing the bond lengths in one of the tables.

Analysing Interactions

Hydrogen bonding

  • Use Olex2’s >>htab command to locate the hydrogen bonds; (use >>help htab to find more information). Type >>htab -g to automatically calculate and generate the resulting hydrogen bonded structure. To return to just viewing the asymmetric unit type >>fuse (note that Olex2 will display HTABs disregarding their validity).

\pi-\pi interactions

To analyse all \pi-\pi interactions associated with the asymmetric unit automatically type >>pipi -g. Type >>fuse to return to the asymmetric unit. This is also available under View|Geometry|Analyse-pi-pi-Interactions.

Locate \pi-\pi interactions manually

  • If the potential \pi-\pi interaction is not within the asymmetric unit, grow the structure to display both parts of the interaction.
  • Select all of the atoms of the first ring under View|Geometry then click on Mean Plane (of active selection). A plane will be displayed in the ring and a centroid generated. All symmetry related planes will automatically be added to any other molecules on the screen.
  • Click on the two centroids under View|Geometry. Click on either Distance and Angles (of selection) or Distance and Angles with esd (of selection), to obtain the distance with or without an esd respectively (the latter requires the use of View|Geometry|Refine-and-save-esd-info first).

Calculating the mean plane of a selection

Select four or more atoms through which to calculate a plane. Click on View|Geometry|Mean-Plane(of-active-selection).

Calculating the deviation of atoms from a plane

Select the atoms to be in a plane and type >>mpln to create the plane. Olex2 to will then print information regarding the plane. If more information regarding this plane is needed, select it and any other object (atom, bond, plane etc) and type >>sel (esd) to get the required information.

Calculating the angle between planes

Create the required planes and select them. In View|Geometry, once again click on either Distance and Angles (of selection) or Distance and Angles with esd (of selection), to obtain the distance with or without an esd respectively. Alternatively:

  • Click on the pencil icon to display the header of the .ins file. On a line below the UNIT instruction, type:
  • >>MPLA X followed by the X atom names in plane 1
  • >>MPLA Y followed by the Y atom names in plane 2.
  • The .lst file will contain information on each plane plus the angle between adjacent planes in the list.

Growing Structures

Olex2 offers a lot of flexibility over the manner in which structures are grown. The majority of these options are found under View|Symmetry-Generation|Growing under which there are three options: Grow, Mode Grow and Assemble.

When completing structures where Z' is not an integer (most commonly Z'=1/2)in Grow mode:

  • Selecting Grow All will display all symmetry equivalent atoms/fragments to display the complete structure. (This is the same as View|Symmetry-Generation|Grow-All).

If the asymmetric unit does not consist of a complete molecule, i.e. Z' is not an integer, this mode will generate the rest of the structure. It is not uncommon for Z' to be some fraction of a molecule, especially if it is sat on or around a special position. In this case the rest of the molecule is generated by one or more symmetry operation(s) e.g. if a molecule is sat on an inversion centre, only half of the molecule will be contained within the ASU. The other half is generated by the inversion centre. For polymeric structures, growth of 1 ASU fragment will occur at each attachment point each time Grow All is clicked on.

  • Shells will grow incomplete fragments atom by atom, shell-by-shell from the currently displayed image.
  • Complete will generate all missing symmetry equivalent atoms of an already grown structure, independent of whether these are bound to the main fragment or not. In other words: all solvent molecules and counter-ions will be generated according to what is already shown.

User-controlled growing modes

These options are similar to grow, but the commands are only executed after you click on an object. When you enter a growing mode, clickable “growing bonds” will sprout from atoms where the kind of growing you have asked for is applicable. There are various options in View|Symmetry-Generation|Growing|Mode-Grow:

  • Short Contacts: Displays growable “bonds” to those atoms where short interactions exist (alternatively type >>mode grow -s). Please note: for this and all other options below, if an atom is selected first, only short interactions to that atom are shown. To exit a mode, press ESC.
  • Contacts near selected atoms - select an atom or atoms and then select Selection to display growable bonds from those atoms. Alternatively type >>mode grow -r.
  • VdW: Contacts within the Van der Waals radii of the atoms will show growable “bonds”. Alternatively type >>mode grow -v *number* where number represents a user specified distance away from atoms.
  • Relocating atoms in the ASU - it may be desirable to select different atoms to form the asymmetric unit. To do this select Move and click on an alternative location.
  • Atom by atom structures can be grown by selecting Shells.

In order to grow all of the displayed, clickable, growing options in growing modes, type >>grow -b.

Reassembling structures

This tool does not strictly belong to the growing family of tools, but it is frequently used together with the growing tools as it allows you to rearrange the asymmetric unit contents into a different configuration. There are various options under View|Symmetry-Generation|Growing|Assemble:

  • Broken Fragments: a structure may become “broken” if parts that should be bonded are shown as separate fragments. This tool will bring them back together (alternatively type >>compaq -a).
  • Atom-to-Atom is very similar to the Broken Fragments tool, but a different algorithm is used (or type >>compaq -c).
  • Metal Last: In this tool, metal ions are ignored while attempts to reassemble the ligand are made. The metal ion is placed at the shortest possible distance. Alternatively, type >>compaq -m.
  • Q-Peaks: This will move all electron density peaks as close to existing atoms as possible (or type >>compaq -q).
  • Growing a structure to display hydrogen bonding interactions:
    • To view the hydrogen bonding interaction associated with the asymmetric unit type >>htab -g. To return to just viewing the asymmetric unit type >>fuse.
  • Displaying the asymmetric unit only:
    • Grow|Asymm.-Unit-(fuse) removes all symmetry equivalent atoms and displays the asymmetric unit. Alternatively type >>fuse.

Packing Structures

Olex2 offers a range of options for packing structures in different ways in order to understand interactions or the lattice packing. These are found under View|Symmetry-Generation|Packing:

  • Adjusting the slider bar under Expand Short Contacts (Hydrogen Bonds) allows short contacts or hydrogen bonding interactions to be displayed. Click on a grow-able link in order to grow a structure. Press ESC to exit this mode.
  • Packing within a defined distance:
    • Can be achieved by moving the slider bar below Pack Radius to display all molecules within a certain distance. Complete fragments are displayed.
    • In order to pack in relation to the unit cell axes, adjust the limits on a, b and c and click on Pack to limits.
    • To display the unit cell contents, click on Fill Unit Cell. This will display all atoms within the unit cell.
    • To complete fragments click on Complete Fragments.

Chemical Tools

Under Tools|Chemical-Tools you will find these useful general tools:

  • CHN Analysis calculates the expected CHN composition on the basis of the unit cell content.
  • Molecular Isotope Pattern simulates a molecular isotope pattern for your structure
  • Molecular Volume - calculates the molecular surface area and molecular volume of the current model.
  • Volume of Polyhedron around Selected Atom calculates the sum of the angles of the selected atom and the tetrahedron volume. This does not apply to terminal atoms.
  • Bounding Box RIGHT CLICK on it and then select Hide to delete it.