jmol enhanced figure toolkit

Introduction Why Jmol? When to use an enhanced figure How to submit an enhanced figure An introductory tutorial Tutorial 2: an inorganic crystal lattice Tutorial 3: a small metal-organic molecule Tutorial 4: a biological macromolecule molecule Toolkit options reference Some Jmol resources Acknowledgements Appendix: useful Jmol commands

Tutorial 3: a small metal-organic molecule

Molecular view with displacement ellipsoids

The 'standard' view of a small-molecule structure determined by X-ray crystallography is typically a minimum-overlap view of a single connected molecule, with atomic displacement tensors represented by real-space probability ellipsoids in the manner of the classic program ORTEP (Johnson, 1965). In this tutorial we demonstrate how to use Jmol to create such a view to the standard normally required for ellipsoid plots by IUCr journals. For this example we use the bromido-1κBr-tricarbonyl-2κ³C-(2η ⁵-cyclopentadienyl)molybdenum(I)tungsten(I)(W-Mo) compound described by Onani et al. (2008). You may follow along with this tutorial by entering the code dn2343 in the toolkit start page (Fig. 4). Remember also to designate this as a small-molecule type of structure from the drop-down menu on that page.

Fig. 25 shows the initial view generated by Jmol. It displays the molecule oriented within the crystallographic unit cell viewed down the c axis, with a running to the right and b upwards. The view is centred on the centroid of the molecule. In this example, the default view is, by good fortune, not far from a minimum-overlap view, but it is not guaranteed to be so. In any case, you will wish to adjust the view for other reasons.

Fig. 25 The on-load view of a small-molecule structure, showing 50% probability ellipsoids.

Begin by rotating the compound through 90° around the z axis, so that the pentacyclodienyl group sits to the upper right. Now zoom in so that the view almost fills the width of the visualization window. (The static figure that is generated for use in the PDF edition will be cropped of surrounding white space, so that filling the view helps to minimize the size difference in the online edition between static and dynamic views.) You should also translate the molecule so that it fits the visualization window most closely (lateral translations are performed in the most common configuration by holding down the CTRL key while dragging with the right mouse button). Fig. 26 shows the result.

Fig. 26 The molecule after repositioning to fill the visualization window.

Now begin to label the figure. Go to the general tab, select the 'atom name' option in the 'Labelling' section, and also select 'monochrome labels'. The result uses an appropriate typeface and font size for the static figure, but the default positioning of many of the labels is poor (Fig. 27). Much of the effort in producing an acceptable primary view of the enhanced figure lies in positioning the labels properly. While the edit palettes provide some tools to help with this, in many cases you will need also to enter explicit commands through the Jmol console.

Fig. 27 {The default labelling options select the appropriate font and type size, but result in many labels that are poorly positioned.

Go to the select/label tab, and choose the 'lower right' option in the set of buttons headed 'Label selected items'. The result is already an improvement (Fig. 28).

Fig. 28 {Placing the labels to the lower right of their corresponding atoms produces an immediate improvement.

Now it is necessary to select individual atoms or groups of atoms which will share the same label offset. It is helpful to toggle 'selection haloes on', which will highlight all the objects selected at any time. When you first do this, you will see that all the atoms are highlighted; so begin by clicking 'none' in the 'Select items' list. Now notice that the labels on all three oxygen atoms just touch their ellipsoids, and would benefit from a slightly greater offset. Click on the 'by element' button of the 'Select items' group, and then click on one of the oxygen atoms. You should find that all three are now highlighted. At this point you should bring up the Jmol console window (right-click in the applet, and choose 'Console' from the pop-up menu - see also Fig. 16). If you click the 'History' button in the console window, you will see the command 'set labeloffset 12 -12' that was invoked when you selected the global 'lower right' option. Enter into the lower window of the console the command 'set labeloffset 14 -14'; you will find that the oxygen-atom labels move slightly, and are now correctly placed (Fig. 29).

Fig. 29 Using the Jmol console window to change the label offset for the current selection (here the three oxygen atoms).

Now you need to fine-tune the other labels. Ensure that you have no atoms currently selected, then click on the 'individual atoms' radiobutton. In this mode, clicking on an individual atom adds it to the currently selected set; clicking on it again removes it from the selection. The following selected sets and corresponding label positioning commands were used to obtain the finished view of Fig. 30:

Fig. 30 The final labelled view with offsets set on an individual basis.

Once you have finished these manipulations, you should ensure that all atoms are selected, then turn off selection haloes before saving the final result (Fig. 30).

Doing other things with ellipsoids

The default for displacement ellipsoids when a CIF is loaded into the toolkit is at probability 50%, solid with a cutout octant and with principal ellipses rendered. Although the principal ellipses are not always apparent at screen resolution, they are more obvious in the high-resolution static figure (Fig. 31).

Fig. 31 The high-resolution static figure displays the principal ellipses more clearly.

Jmol also provides different styles of rendering, accessed through the options on the ellipsoids tab. These include solid ellipsoidal volumes and various simplified representations showing only midplanes, principal ellipses or principal axes. Although these are not generally suitable for the main view of the molecule, they can be helpful in different enhanced views, especially for large molecules or packing diagrams where the computational burden of rendering solid ellipsoidal volumes is high. There is also an option for displaying the wireframe outlines of the ellipsoids (or other solid objects) while the model is being manipulated. This can make it much easier and faster to select a particular orientation before implementing the full rendering.

Note that the default loading renders hydrogen atoms as small spheres, but the ellipsoid tab provides options for suppressing the display of H atoms altogether, or of showing their ellipsoids.

Note also that the ellipsoid properties are assigned to all the atoms in the current selection. This means that you could select different parts of the structure and supply them with different probability ellipsoids, or as simple spheres or sticks (useful, for example, in de-emphasising large ellipsoids associated with poorly refined solvent molecules). Such selective modifications should of course be detailed in a caption.

Another useful option is the ability to colour 'by temperature'. In practice, this is a graduated colour scale running from blue ('cold') through red to white in accordance with the modulus of the displacement amplitude. It can provide additional visual cues to interpreting the displacement behaviour of the atoms in the structure.

Fig. 32 shows a view of the structure normal to the cyclopentadienyl ring. Here the ellipsoids are shown at 60% probability, coloured in proportion to their mobility. The ellipsoids have also been made translucent, so that one may see embedded atom spheres, colour coded by element. The torsional motion of the Cp ring is clear, and especially its asymmetric nature. The relatively large motions of the two terminal oxygens are also immediately obvious.

Fig. 32 Use of colour and higher-probability ellipsoid envelopes to emphasise the mobility within the compound.

Complementary styles of representation

This example shows how to produce an unusual representation illustrating the molecular displacements of the crystal packing (Fig. 33). We simply outline the procedures here; reproducing the details is left as an exercise for the reader.

Fig. 33 Molecular motions within the cell packing.

On the crystallography tab, select a cell packing range (2 x 2 x 1 was chosen in this example). The default cell packing rendering is ball-and-stick; leave that unchanged. Using the select/label tab, select the individual molecules surrounding the one that you wish to emphasise. Assign them 100% van der Waals atom radii and colour them distinctively. It may be necessary to select one of the space-filling molecules and conceal it in order to see the molecule of interest sitting in the pocket formed by its neighbours. There are several ways of hiding a molecule, some of which interfere with other items in a current selection. Perhaps the safest way is to select the molecule, then choose 'atoms off' and 'bonds off' for that molecule.

Finally, deselect everything and then select the central molecule. Using the ellipsoid tab, render 60% probability ellipsoids and colour the molecule by displacement modulus.

When you are happy with the result, save the current view into a button script (see Fig. 13) and enter a suitable caption. Now save the new view using the secondary save button ('Save updates to scripts only').

The result not only illustrates how an individual molecule is free to rotate and stretch within the steric constraints of its neighbours, but allows the reader to zoom out and appreciate how the molecules sit in relation to the large-scale order of the crystal symmetry.

Example 3 Click on the thumbnail to launch the enhanced figure in a separate window.