Represent bonds spanning a unit cell boundary plane

Question

Is there a chemical input format that is-

1. Supported by Open Babel (and hence supports visualization in avogadro??)
2. Can represent a bond connecting an atom to its partner in a neighbouring unit cell, for crystals/systems with periodic boundary conditions

Follow up (added later):

I could not understand how cif does it, or cml. But it would be nice if I could get rid of the symmetry folds in the markup given below.

Here is the cif file. The cml output using babel is --

<?xml version="1.0"?>
<molecule id="Calcium titanate" xmlns="http://www.xml-cml.org/schema">
 <crystal>
  <scalar title="a" units="units:angstrom">5.380000</scalar>
  <scalar title="b" units="units:angstrom">5.440000</scalar>
  <scalar title="c" units="units:angstrom">7.639000</scalar>
  <scalar title="alpha" units="units:degree">90.000003</scalar>
  <scalar title="beta" units="units:degree">90.000003</scalar>
  <scalar title="gamma" units="units:degree">90.000003</scalar>
  <symmetry spaceGroup="-P 2c 2ab">
   <transform3>1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1</transform3>
   <transform3>1 0 0 0.5 0 -1 0 0.5 0 0 -1 0 0 0 0 1</transform3>
   <transform3>-1 0 0 0 0 -1 0 0 0 0 1 0.5 0 0 0 1</transform3>
   <transform3>-1 0 0 0.5 0 1 0 0.5 0 0 -1 0.5 0 0 0 1</transform3>
   <transform3>-1 0 0 0 0 -1 0 0 0 0 -1 0 0 0 0 1</transform3>
   <transform3>-1 0 0 0.5 0 1 0 0.5 0 0 1 0 0 0 0 1</transform3>
   <transform3>1 0 0 0 0 1 0 0 0 0 -1 0.5 0 0 0 1</transform3>
   <transform3>1 0 0 0.5 0 -1 0 0.5 0 0 1 0.5 0 0 0 1</transform3>
  </symmetry>
 </crystal>
 <atomArray>
  <atom id="a1" elementType="Ti" formalCharge="4" xFract="0.000000" yFract="0.500000" zFract="0.000000"/>
  <atom id="a2" elementType="Ca" formalCharge="2" xFract="0.006480" yFract="0.035600" zFract="0.250000"/>
  <atom id="a3" elementType="O" formalCharge="-2" xFract="0.571100" yFract="-0.016100" zFract="0.250000"/>
  <atom id="a4" elementType="O" formalCharge="-2" xFract="0.289700" yFract="0.288800" zFract="0.037300"/>
 </atomArray>
 <bondArray>
  <bond atomRefs2="a1 a4" order="1"/>
  <bond atomRefs2="a4 a2" order="1"/>
 </bondArray>
</molecule>

Answer 1

As the developer of both Open Babel and Avogadro I can say the answer is "not yet."

The main thing isn't the file format. It's that Avogadro at the moment doesn't have support at the moment to show bonds across a unit cell.

I believe there was a patch for that, but it was too slow for typical use: https://github.com/dlonie/avogadro/commits/ENH_intercell_bonds

Answer 2

As pointed out by Geoff Hutchinson, this isn't currently possible by Avogadro and OpenBabel - and he should know best ;)

Since you want to visualize a feature of crystalline systems, you might want to have a look at specialized programmes that predominantly/only operate on CIF files. We have used SCHAKAL, written by Egbert Keller, for this purpose in the past.

Out of my mind, I don't remember how it was done. But it can be done, just like almost anything else you can imagine, such as centroid-centroid bonds between rings, etc.

Be warned: SCHAKAL's GUI violates any design rules (even if you apply Klingon standards). Once you have it compiled and running, switch the GUI off and operate it through chains of unituitive one-key shortcut commands. If you have overcome the horrors, you'll be rewarded with a fantastic postscript output in publication quality.