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While there are a few tools for visualizing crystal structures, I'm particularly curious to know tools for visualizing space group symmetry, including:

  • screw axes
  • glide planes

I teach a class on molecular symmetry and would like to expand to teaching about space groups. It's relatively easy to depict mirror planes and inversion centers, but glide planes and screw axes are a bit harder for chemists to visualize.

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  • $\begingroup$ And yes, if possible, I'd love to implement these in Avogadro v2, so there are multiple reasons for the question... $\endgroup$ – Geoff Hutchison May 4 at 18:40
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    $\begingroup$ This is not a tool, but last year when I had to study crystal structure, I found Frank Hoffmann's videos on Youtube quite helpful. In those videos, the glide plane and screw axes are explained by an animation, which I think explains those quite clearly: e.g.- youtube.com/watch?v=5XwZj0m8zEQ $\endgroup$ – Shoubhik R Maiti May 4 at 19:02
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    $\begingroup$ Also not a tool, but I like how a screw-axis symmetry is illustrated in Fig. 2 of nature.com/articles/nphys2600 $\endgroup$ – Anyon May 4 at 19:20
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Jmol/JSmol

Did you consider Jmol/JSmol? It is freely available for Windows / Mac / Linux, scriptable, may export what is being displayed in formats relevant to chemistry (e.g., .pdb, .sdf), as image (e.g., .png, .pngj, [animated] .gif) and already is in use to teach symmetry in molecules and crystals. As an example, the interactive compilations by Symmetry@Otterbein dedicate a page about a few space groups, too. Jmol/JSmol is a default viewer of the 3D structures of the IUCr Journals, and there is a forum dedicated to its use in crystallography, too.

In 2010JApplCryst1250 Hanson presents a selection of what may be achieved. This open access publication offers all the data to replicate the figures displayed in the publication as SI, too. For example:

enter image description here

enter image description here

enter image description here

Much of this may be tried out -- just from the browser -- in a dedicated test site.

In a period of extended distance learning, earlier publications in the Journal of Chemical Education about this program (like 2005JChemEduc1736, or 2007JChemEduc2475) may be of general interest, too.

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  • $\begingroup$ These are helpful - and I recall having discussions with Bob about crystal visualization. At the moment, the Otterbein site doesn't have the crystallography features -- I think because the molecule point group features now use NGL instead of JSmol. IIRC neither NGL or 3DMol.js have yet implemented CIF / space group features. $\endgroup$ – Geoff Hutchison May 5 at 15:38
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CCDC Mercury

The Cambridge Crystallographic Data Centre (CCDC) provides a free-to-use visualization program Mercury that offers a wide variety of features for crystal structures including, perhaps not surprisingly crystallographic symmetry.

The trick, of course, is to have appropriate crystal structures to illustrate points. CCDC does provide a free teaching subset which includes fundamental chemistry (e.g., molecular shapes / VSEPR) and symmetry.

Glide Planes

Here's a similar illustration of the "c" glide plane in maleic acid:

Glide plane in maleic acid

Screw Axis

Here's an illustration of chloromethane $Cmc2_1$ illustrating the multiple screw axes:

enter image description here

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  • $\begingroup$ I agree that CCDC's Mercury program offers many functions including these and it may be nice to click (after using it for a while you get to know (muscle memory) where the functions are.) A scripted approach, however, offers a trail how to do / what was done (reproducible research). However, Mercury basically is one program, regardless if opting for the free community version (overview) or the the one within the (then to pay) CCDC suites; the number of menu entries then grayed out differs in function of the software key you have for a heavy weight. $\endgroup$ – Buttonwood 2 days ago
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    $\begingroup$ (part 2:) I do not know the IT infrastructure at disposition for your (assumed to be) remote attendees. Note, even the current, free community version of Mercury (standalone), eats 1.6 GB HDD, and needs 8 GB RAM for smooth work. Jmol is just the .zip from sf; once unzipped (portable, e.g. on an USB thumbdrive) and ready to go on less powerful / older computers backed by java with a total of just 57MB (as by du -h on jmol-14.31.32). A less number of buttons to click, but there are script tutorials. $\endgroup$ – Buttonwood 2 days ago
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    $\begingroup$ @Buttonwood - I completely agree that Mercury has issues, and JSmol is a great tool. My main complaint with JSmol is the rendering quality - I'd love if Bob would consider a version that used WebGL which would greatly improve that. But I think it's important for the site to include multiple options. $\endgroup$ – Geoff Hutchison 2 days ago
  • $\begingroup$ I'm not familiar with the inner of Jmol, but there its wiki has a dedicated page about WebGL thus allowing insight and contribution to improve the working. But I agree, chem.se should present more than one option if there are, as none of the programs may offer all. As for the data to teach with and about, complementary to the CCDC teaching subset are, for example, the entries of the COD which likely would welcome if you could initiate a mirror in the US. $\endgroup$ – Buttonwood 2 days ago
  • $\begingroup$ @Buttonwood - I wondered at your file size for Mercury.. Turns out it includes an anaconda Python 3.6 install. imgur.com/Zsr2xTp $\endgroup$ – Geoff Hutchison 2 days ago

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