# Heuristic for Reading CIF / Crystal Structures? **URL:** \ **Category:** General Discussion\ **Created:** [November 7, 2011, 5:05pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214 "2011-11-07T17:05:20Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [November 7, 2011, 5:05pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214/1 "2011-11-07T17:05:20Z")
Hi, As some of you know, in the long-awaited v1.1 release, there’s significantly improved solid-state and CIF support. This is, in no small part, due to work by David Lonie and his crystallography extension. To further improve, I’m thinking of a heuristic when reading CIF (and other) crystallography files to separate between “molecular crystals” and solid-state crystals. - For molecular crystals the user often (but not always) wants the primitive unit cell – just an isolated molecule. To fill out the entire cell, it’s OK to have a separate command. - For solid-state crystals, the user usually wants to see the entire unit cell, including all symmetry-defined positions. Now this type of heuristic seems to be in use by other programs like Mercury (from the CCDC) and CrystalMaker, IIRC. I’m proposing that when Avogadro reads a file (through File -\> Open) it decides if it’s likely a molecular crystal if: - There’s a unit cell (i.e., it’s a crystal) - It has at least one carbon, AND at least one hydrogen in the primitive cell - OR it has at least five carbons (e.g., benzene, pyridine, etc. with no hydrogens defined) in the primitive cell I’m open to suggestions – I’d like to include as many molecular crystals without picking up carbonates or carbides. Thoughts? -Geoff * * * Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: [geoff.hutchison@gmail.com](mailto:geoff.hutchison@gmail.com) web: [http://hutchison.chem.pitt.edu/](http://hutchison.chem.pitt.edu/) ---
**Author:** ![allison.vacanti](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/allison.vacanti/32/112_2.png) [@allison.vacanti](https://discuss.avogadro.cc/u/allison.vacanti)\ **Post date:** [November 7, 2011, 5:45pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214/2 "2011-11-07T17:45:18Z")
On Mon, Nov 7, 2011 at 12:05 PM, Geoffrey Hutchison [geoff.hutchison@gmail.com](mailto:geoff.hutchison@gmail.com) wrote: > I’m proposing that when Avogadro reads a file (through File → Open) it decides if it’s likely a molecular crystal if: > > - There’s a unit cell (i.e., it’s a crystal) > - It has at least one carbon, AND at least one hydrogen in the primitive cell > - OR it has at least five carbons (e.g., benzene, pyridine, etc. with no hydrogens defined) in the primitive cell > > I’m open to suggestions – I’d like to include as many molecular crystals without picking up carbonates or carbides. I see what you’re saying. Perhaps we could screen for elements besides C,H,N,O,S – If all atoms are common organic elements, it is probably just a molecular packing and we can stick with the primitive structure, but if there are, say, transition metals, present then the full cell is probably of interest. I should also point out that I don’t work with molecular crystals very much, so my use-cases are imaginary 😉 Dave ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [November 7, 2011, 5:50pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214/3 "2011-11-07T17:50:06Z")
On Nov 7, 2011, at 12:45 PM, David Lonie wrote: > > I’m open to suggestions – I’d like to include as many molecular crystals without picking up carbonates or carbides. > > I see what you’re saying. Perhaps we could screen for elements besides > C,H,N,O,S – If all atoms are common organic elements, it is probably > just a molecular packing and we can stick with the primitive > structure, but if there are, say, transition metals, present then the > full cell is probably of interest. That doesn’t work so well. Consider ferrocene, or any organometallic (molecular) catalyst. This is why I recommend a certain number of carbons in the primitive cell → probably a molecular crystal. -Geoff ---
**Author:** ![allison.vacanti](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/allison.vacanti/32/112_2.png) [@allison.vacanti](https://discuss.avogadro.cc/u/allison.vacanti)\ **Post date:** [November 7, 2011, 6:15pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214/4 "2011-11-07T18:15:51Z")
On Mon, Nov 7, 2011 at 12:50 PM, Geoffrey Hutchison [geoff.hutchison@gmail.com](mailto:geoff.hutchison@gmail.com) wrote: > On Nov 7, 2011, at 12:45 PM, David Lonie wrote: > > > > I’m open to suggestions – I’d like to include as many molecular crystals without picking up carbonates or carbides. > > > > I see what you’re saying. Perhaps we could screen for elements besides > > C,H,N,O,S – If all atoms are common organic elements, it is probably > > just a molecular packing and we can stick with the primitive > > structure, but if there are, say, transition metals, present then the > > full cell is probably of interest. > > That doesn’t work so well. Consider ferrocene, or any organometallic (molecular) catalyst. This is why I recommend a certain number of carbons in the primitive cell → probably a molecular crystal. I guess my question is: when is the full cell of interest, and when is unfilled cell desired? The way I’m thinking about it, if it is just a simple organic molecule then the unfilled cell will suffice. If there’s anything else going on besides VDW/H-bonding in a simple organic crystal, then I’d want to see the full structure (this includes organometallics). As you mention, carbonates etc will pose a problem otherwise. I’d rather make the mistake of filling a cell when the unfilled cell is sufficient then the other way around. Is the problem with a filled molecular crystal cell just that it’s difficult to see what’s going on (too much info)? If so, I think that some of the visualization tricks I’ve been working on for intercellular bonding may be a better solution, instead of presenting an unfilled cell. (I have plans to add improved intercell bond visualization in the coming months. I’ll post an update once I have some stable code.) Dave ---
**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\ **Post date:** [November 8, 2011, 8:40pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214/5 "2011-11-08T20:40:13Z")
> Is the problem with a filled molecular crystal cell just that it’s > difficult to see what’s going on (too much info)? That’s part of it, but also users often just want “the experimentally-derived” molecular structure. So maybe I synthesize a compound, get the x-ray structure and a CIF. I don’t want the full unit cell – I probably just want the molecule to paste into a manuscript or presentation, or maybe to submit to Gaussian. So there really are two different use cases – I’m opening a file because it has x-ray defined coordinates of my molecule VS I’m opening a crystal and want to see the whole unit cell. Thus the need for a decent heuristic. It won’t always work – I might open benzene and want the whole unit cell, or I might want the primitive coordinates for YBCO. Fortunately, we have ways of handling that already. I just want the default experience to be good. Hope that makes sense. -Geoff ---
**Author:** ![allison.vacanti](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/allison.vacanti/32/112_2.png) [@allison.vacanti](https://discuss.avogadro.cc/u/allison.vacanti)\ **Post date:** [November 10, 2011, 4:04pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214/6 "2011-11-10T16:04:39Z")
On Tue, Nov 8, 2011 at 3:40 PM, Geoffrey Hutchison [geoff.hutchison@gmail.com](mailto:geoff.hutchison@gmail.com) wrote: > > Is the problem with a filled molecular crystal cell just that it’s > > difficult to see what’s going on (too much info)? > > That’s part of it, but also users often just want “the experimentally-derived” molecular structure. So maybe I synthesize a compound, get the x-ray structure and a CIF. I don’t want the full unit cell – I probably just want the molecule to paste into a manuscript or presentation, or maybe to submit to Gaussian. > > So there really are two different use cases – I’m opening a file because it has x-ray defined coordinates of my molecule VS I’m opening a crystal and want to see the whole unit cell. > > Thus the need for a decent heuristic. It won’t always work – I might open benzene and want the whole unit cell, or I might want the primitive coordinates for YBCO. Fortunately, we have ways of handling that already. I just want the default experience to be good. Ok – that works for me. My biggest concern with not showing the full unit cell is that, as Avogadro is educational software, students may not realize that they’re only seeing part of the structure. So some sort of notification may be useful here. A popup or slim dockwidget with a “don’t show me again” checkbox informing the user that a reduced representation is being shown would be a nice touch. I could add some API to the crystallography extension that would return the Fill Unit Cell QAction, so that we could even give the option of filling the cell from the popup. Dave ---
**Author:** ![Louis\_Ricard](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/l/b77776/32.png) [@Louis\_Ricard](https://discuss.avogadro.cc/u/Louis_Ricard)\ **Post date:** [November 10, 2011, 7:46pm UTC](https://discuss.avogadro.cc/t/heuristic-for-reading-cif-crystal-structures/214/7 "2011-11-10T19:46:06Z")
Hi all. A brief comment. The cif file contains only the asymmetric unit content. So, if a user wants to see “my molecule”, only part of it will be displayed when opening a cif or res file in Avo, at present. This depends on the way connectivity is generated and is complicated by the fact that it may well be an infinite structure. In other words, displaying a crystal without taking site symmetries into account will produce incomplete coordinates for use in QM programs. Louis Le 10 nov. 2011 à 17:04, David Lonie a écrit : > On Tue, Nov 8, 2011 at 3:40 PM, Geoffrey Hutchison > [geoff.hutchison@gmail.com](mailto:geoff.hutchison@gmail.com) wrote: > > > > Is the problem with a filled molecular crystal cell just that it’s > > > difficult to see what’s going on (too much info)? > > > > That’s part of it, but also users often just want “the experimentally-derived” molecular structure. So maybe I synthesize a compound, get the x-ray structure and a CIF. I don’t want the full unit cell – I probably just want the molecule to paste into a manuscript or presentation, or maybe to submit to Gaussian. > > > > So there really are two different use cases – I’m opening a file because it has x-ray defined coordinates of my molecule VS I’m opening a crystal and want to see the whole unit cell. > > > > Thus the need for a decent heuristic. It won’t always work – I might open benzene and want the whole unit cell, or I might want the primitive coordinates for YBCO. Fortunately, we have ways of handling that already. I just want the default experience to be good. > > Ok – that works for me. My biggest concern with not showing the full > unit cell is that, as Avogadro is educational software, students may > not realize that they’re only seeing part of the structure. So some > sort of notification may be useful here. A popup or slim dockwidget > with a “don’t show me again” checkbox informing the user that a > reduced representation is being shown would be a nice touch. I could > add some API to the crystallography extension that would return the > Fill Unit Cell QAction, so that we could even give the option of > filling the cell from the popup. > > Dave > > * * * > > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > [http://p.sf.net/sfu/rsa-sfdev2dev1](http://p.sf.net/sfu/rsa-sfdev2dev1) > > * * * > > Avogadro-devel mailing list > [Avogadro-devel@lists.sourceforge.net](mailto:Avogadro-devel@lists.sourceforge.net) > [avogadro-devel List Signup and Options](https://lists.sourceforge.net/lists/listinfo/avogadro-devel)