# FAQ

## General​

See: How to cite

### Why does my Licence not work?​

The best approach is to cut and paste the licence information directly from the email we sent to you, to minimise any mistakes in copying.

Sometimes there can be issues with the encoding (UTF-8 vs. UTF-16) of special characters, for this reason we recommend you register using only ASCII characters.

If you still have problems please email us and we'll help.

### What are the Licence Conditions for CrystalExplorer?​

See: Licensing for the details, but in short it's free for academic purposes, and non-free for commercial purposes.

## Using CrystalExplorer​

### Why have the X-H bond lengths changed in my structure?​

CrystalExplorer normalizes the X-H bond lengths to be the same as those obtained from a neutron diffraction experiments since those obtained from X-ray diffraction experiments are typically several tenths of an Å shorter than the correct lengths.

Neutron Bond Lengths:

Bond TypeBond Type
C-H1.083
N-H1.009
O-H0.983
B-H1.180

By normalizing these bond lengths the Hirshfeld surface obtained is independent of the method used to determine the structure and allows meaningful comparisons to be made. Since CrystalExplorer is often used to analyze intermolecular interactions it is especially important to standardize the X-H distances.

### Why does CrystalExplorer complain that my structure has an element beyond Xe?​

If you want to generate surfaces or map surface properties which require a wavefunction on structures containing trans-Xe elements the Clementi-Roetti basis-set is insufficient and you must use the Thakkar basis-set. You can choose the Thakkar in Preferences→Expert Settings→Atomic Wavefunction Type.

### Why doesn't my CIF load?​

Many of the crystallographic programs in use today don't create CIFs that adhere to the standard. This causes problems for CrystalExplorer. If you are having problems with your CIF we advise you to run it through IUCr's CIF checking service and addressing the issues that come up.

Another good workaround we have found is the first load up a CIF in Mercury and then resave the CIF. Mercury is very good at dealing with non-standard CIFs and is in general able to convert them correctly.

### The graphical display is unusably slow​

This is likely an issue with graphics drivers, related to our use of the fixed-function OpenGL pipeline. A rendering rewrite is in the works, but it is not yet complete.

We've noted that this typically occurs on integrated Intel graphics, or AMD graphics cards. One of the bottlenecks is the software emulation of picking objects in the drivers - this is particularly bad on AMD graphics cards on Linux. One workaround is to use the middle click (which does not trigger a pick event) to rotate the scene, rather than left clicking.

### How do I export graphics for figures/How can I export a PNG?​

In previous versions of CrystalExplorer (before CrystalExplorer17), there was an option to render the display to an image - this was no longer working (and fixing it involved rewriting the renderer) so it has been disabled.

We typically use screenshots or screengrabbing tools in order to export the figures for publication.

It is worth noting that the previous feature did not export an image at a higher resolution than was currently being displayed in any case, so the end result should be equivalent.

## Common Issues​

### CrystalExplorer can't find the Tonto executable​

Assuming that CrystalExplorer was installed correctly, the Tonto executable should be packaged with it. However, the setting of where to located may be incorrect (either via installation, a previous version or it's been changed by the user).

To resolve this, you can navigate to the Preferences pane via File→Preferences, then under the Expert tab there is a setting for The Tonto executable.

One option is to click Restore Expert Settings and then it will set whatever the default path is.

If this doesn't work, try clicking Set Path, then navigating to wherever CrystalExplorer is installed (probably C:\Program Files\CrystalExplorer on Windows) and in the resources directory there should be a tonto executable, either called tonto (MacOS/Linux) or tonto.exe (Windows).

If this setting points to this executable then it should work.