Reports & Images

Every structure determination needs reports and images. Here’s how you get them using Olex2

Tools for the creation of images are available from Tools|Images.

Labelling Atoms

Labels can be placed on either atoms or bonds (or a mixture of both).

  • If no atoms (or bonds) are selected, all atoms and bonds will be labelled. Clicking non-H atoms will label all of the non-hydrogen atoms. If symmetry-equivalent atoms are shown, their symmetry label will be printed according to the Symm and Style options.
  • Labels can be moved, individually or in groups, while holding down the SHIFT key and the LEFT MOUSE button and moving the mouse.

Deleting labels

Labels can be deleted:

  • Individually, by selecting an atom label with the LEFT MOUSE button and pressing DELETE.
  • Double click on any label to select them all, then press DELETE.

There are two independent sets of labels. The built-in labels (toggled with F3 and under Work|Toolbox-Work) and then those accessed from Tools|Images. These image labels can be positioned with SHIFT + LEFT MOUSE. The built-in labels are useful if you want to see to see all atom names, but label only a few atoms.

Generating Figures

A variety of options are available for creating figures are available under View|Quick-Drawing-Styles and Tools|Images. Pictures are created of the molecules or fragments displayed on the graphics screen and can either be of a grown or ungrown structure.

Creating and Saving Images

Olex2 offers a number of different file formats for saving images, these are found under Tools|Images. A name for the structure image can be typed into the white box. There are options to specify what happens if an image file already exists, the default is to Ask, but it is also possible to select Increment or Replace from the drop-down menu. A number of other options are available:

  • Label selected - will label all the selected atoms and/or bonds. If none are selected, then all bonds and atoms will be labelled.
  • Non-H atoms - will label all atoms that are not hydrogens.
  • DELETE all labels - deletes any labels shown.
  • Choose the label colour and Label Box - allows you to customise the labels and label box by changing their colour, transparency etc.
  • Align - Clicking on View will show the structure with the largest number of atoms visible on the screen. Clicking on Plane will show the view with the best plane through the structure.
  • Lock all - Ticking this box locks the structure so it cannot be zoomed, rotated or translated. Unticking any of the boxes will reinstall the feature.

There are a number of further image customising and saving options under Tools|Images:

  • Bitmap Images - will create a bitmap image of the structure by clicking Go.
    • Selecting Trim will trim the image depending on the Padding selected (greater padding means a larger distance between the structure and edge of crop in the final image).
    • There is an option to add a Border and customise its Colour. Click Add Fog to change the definition of the structure and use the Front and Back slider bars to customise this. Clear Fog will remove the fog effect and return to showing the normal image.
    • There is also an option to change the Atom (Atom Label Font (Olex2)) and Bond (Bond Label Font (Olex2) label fonts from a saved file. Clicking System Font allows different fonts to be selected.
  • Postscript Images - creates a postscript image in ORTEP style. Click Go to create the image. There are numerous options to edit the image including:
    • Atoms: Change the outline width.
    • Octant: Specify the number of dividers within the Octant drawn.
    • Fonts and Bond Font: Modify the font styles for the labels.
  • Povray Images - Olex2 writes a .pov file for the image. Click Go to create the image. Note that any further changes need to be made using PovRay software.
  • Image Series - creates a series of images for a movie. There are options for changing the Rotation around Axis, the number of degrees of rotation between each image, the Number of Frames and the Size. Click Go to create the image.

Changing the atom display style

The same display options apply for changing the appearance of the atoms during a refinement as can be used for generating images. These can be found under View|Quick Drawing Styles. Alternatively, right click on the graphics display window and under Draw Style select the desired appearance.

When producing figures there may be conventions for expected formats, e.g. for small-molecule organic and organometallic compounds an ellipsoid plot is typical with carbon atoms grey, oxygen red. In such cases, it is a good idea to follow convention. In other situations the appearance of the figures may be down to the personal preference.

Writing a Report or a CIF

Olex2 generates both a report, containing crystallographic information in table format typical for papers, and a standard CIF, using user controlled values. The options available under Work|Report are relatively self-explanatory and hence this section is not discussed in detail here.