High-quality figures in Mercury for article/poster/presentation

Figures in scientific articles can be considered as a separate type of art. As a rule, if your figures are quite clear, the reviewer/reader has no doubts or claims about them.

The main rule sounds like this – when someone is viewing your drawing, the person should not experience stress, and if possible get aesthetic pleasure.

There is a small article on how it can be done in a crystal structure visualizer – Mercury (V.2021.1.0). You can download the program on the website of The Cambridge Crystallographic Data Centre (it requires registration). Here you can find the full Mercury user guide.

Settings

If you don’t want to bother too much with this, you can use my style settings. Unpack it, then go to Display/Manage Styles/Open and choose Mercury_style.msd.

Otherwise, you have to go to Style Manager as well, but change them manually:

Display/Manage Styles/Edit

Everything is intuitive here. I’d like to draw your attention to Ellipsoid Settings. The Probability level should be 30-50%, in this case, it remains possible to visually judge the quality of the structure.

Finding the optimal view of the structure

Once you’ve opened your structure file (cif, res, ins also support mol, pdb, xyz) it’s time to find the best angle. Here are some basic guidelines with examples:

1. It’s advisable to select a view in such a way that the bonds between atoms are not intersected and atoms do not obscure each other or it is reduced to a minimum.

2. In the case of organometallic compounds, the coordination polyhedron should be visible.

3. If hydrogen atoms are not so important, they can be hidden as well as solvent molecules.

4. If your drawing contains too many atoms, leading to clutter and overlap, you can simplify the structure by representing certain groups (like -tBu, -Ph, -Ar) with lines. If that’s still too complex, you can remove those groups entirely and replace them with text-based symbols.

All of the figures were taken from the article: 10.1039/D1DT00717C

Labeling atoms

In order to sign the labels of atoms, there are two options:

1. You can save the picture and then add the positions of the symbols in other graphical editors. The advantage of this approach is the ability to quickly change the font, size and positions of labels in future (especially if it supports layers), but it’s more time-consuming.
   
2. This can be done directly in Mercury. Note that there is no option here to save this as an editable file. If you agree go to Display/Display options/Labels. You can choose any colour, size and font of labels.

Then on the Display options panel (make sure it is displayed: Display/Toll bars/Display options) check the box next to Label Atom. On the top panel Picking toolbar choose Move Labels and then move the labels to the desired positions.

Render

When you’ve found the best view and key atoms have labels you can start the render: File/Pov-Ray Image

1. Set up the resolution (I recommend using a little bit higher than you need).
2. You can play with Material Properties, but Standard Mercury is good as well.
3. If your background is not white you can use PNG in File Format and Transparent in Background.
4. Choose your output folder and click Render (or Preview to be sure that the structure is not cut).

Animation

Static images have a big disadvantage – they are very dependent on the point of view. Rotation animation can be used to show your entire structure during a presentation. On the Animation Toolbar panel push the Animate Structure button, then play with axes and other parameters.

When you will find the best position stop it and go to Pov-Ray Image. Сheck the box next to Generate Animation Frames, choose the axe and set up the number of frames. The more frames the animation will look smoother, but the more time will be spent and, as a result, the file size will increase. In order not to render the background, I recommend using a transparent one. For example, there are two files for comparison of 60 and 180 frames:

Preparation of Gif file

Now it’s time to merge your frames into the Gif-file. There are many software and online services for it. I can recommend PhotoScape X it’s quite a simple and free-of-charge programme. After installing the program, open the render folder and select all the frames (Ctrl + A), then just place them in the middle part while holding the left mouse button. When transferring, a window with a transparency level will appear, if you use a transparent background when rendering, you can accept the default settings. After that, change the Duration and Size, when it’s done click Save in the lower right corner.

Practical tricks

There are several useful tricks for the preparation of figures.

Dotted coordination bond

If you already have a bond line between two atoms, you can make left click Show/Hide – Hide, then Use Picking Mode-Measure Distances and select two atoms. Afterwards, change Picking Mode to Move labels and move all distances away. Right-click on the dotted line and change Color, Thickness and Style as you want.

Short contacts

In the case of cristal packing analysis, you simply can use Display Options – Packing. But in some cases, you will need only several molecules around the central one. In this respect better to use the check box Short Contact and H-Bond. Then you can expand desired contacts (Picking Mode – Expand Contacts).

Selection of atoms

If you would like to hide all of the H-atoms but keep several of them there is an easy way how to do it. Go to Display – More information – Atom list. There is a table with all of the atoms. Sort it by Label and select all of H (click on the first one, then hold Shift and click on the last one). Now If you go back to the main screen you will find that all of the H atoms are selected, deselect some of them and right-click Show/Hide–Hide atoms.