Represent bonds spanning a unit cell boundary plane Is there a chemical input format that is-

Supported by Open Babel (and hence supports visualization in avogadro??)
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 --
&lt;?xml version=&quot;1.0&quot;?&gt;
&lt;molecule id=&quot;Calcium titanate&quot; xmlns=&quot;http://www.xml-cml.org/schema&quot;&gt;
 &lt;crystal&gt;
  &lt;scalar title=&quot;a&quot; units=&quot;units:angstrom&quot;&gt;5.380000&lt;/scalar&gt;
  &lt;scalar title=&quot;b&quot; units=&quot;units:angstrom&quot;&gt;5.440000&lt;/scalar&gt;
  &lt;scalar title=&quot;c&quot; units=&quot;units:angstrom&quot;&gt;7.639000&lt;/scalar&gt;
  &lt;scalar title=&quot;alpha&quot; units=&quot;units:degree&quot;&gt;90.000003&lt;/scalar&gt;
  &lt;scalar title=&quot;beta&quot; units=&quot;units:degree&quot;&gt;90.000003&lt;/scalar&gt;
  &lt;scalar title=&quot;gamma&quot; units=&quot;units:degree&quot;&gt;90.000003&lt;/scalar&gt;
  &lt;symmetry spaceGroup=&quot;-P 2c 2ab&quot;&gt;
   &lt;transform3&gt;1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1&lt;/transform3&gt;
   &lt;transform3&gt;1 0 0 0.5 0 -1 0 0.5 0 0 -1 0 0 0 0 1&lt;/transform3&gt;
   &lt;transform3&gt;-1 0 0 0 0 -1 0 0 0 0 1 0.5 0 0 0 1&lt;/transform3&gt;
   &lt;transform3&gt;-1 0 0 0.5 0 1 0 0.5 0 0 -1 0.5 0 0 0 1&lt;/transform3&gt;
   &lt;transform3&gt;-1 0 0 0 0 -1 0 0 0 0 -1 0 0 0 0 1&lt;/transform3&gt;
   &lt;transform3&gt;-1 0 0 0.5 0 1 0 0.5 0 0 1 0 0 0 0 1&lt;/transform3&gt;
   &lt;transform3&gt;1 0 0 0 0 1 0 0 0 0 -1 0.5 0 0 0 1&lt;/transform3&gt;
   &lt;transform3&gt;1 0 0 0.5 0 -1 0 0.5 0 0 1 0.5 0 0 0 1&lt;/transform3&gt;
  &lt;/symmetry&gt;
 &lt;/crystal&gt;
 &lt;atomArray&gt;
  &lt;atom id=&quot;a1&quot; elementType=&quot;Ti&quot; formalCharge=&quot;4&quot; xFract=&quot;0.000000&quot; yFract=&quot;0.500000&quot; zFract=&quot;0.000000&quot;/&gt;
  &lt;atom id=&quot;a2&quot; elementType=&quot;Ca&quot; formalCharge=&quot;2&quot; xFract=&quot;0.006480&quot; yFract=&quot;0.035600&quot; zFract=&quot;0.250000&quot;/&gt;
  &lt;atom id=&quot;a3&quot; elementType=&quot;O&quot; formalCharge=&quot;-2&quot; xFract=&quot;0.571100&quot; yFract=&quot;-0.016100&quot; zFract=&quot;0.250000&quot;/&gt;
  &lt;atom id=&quot;a4&quot; elementType=&quot;O&quot; formalCharge=&quot;-2&quot; xFract=&quot;0.289700&quot; yFract=&quot;0.288800&quot; zFract=&quot;0.037300&quot;/&gt;
 &lt;/atomArray&gt;
 &lt;bondArray&gt;
  &lt;bond atomRefs2=&quot;a1 a4&quot; order=&quot;1&quot;/&gt;
  &lt;bond atomRefs2=&quot;a4 a2&quot; order=&quot;1&quot;/&gt;
 &lt;/bondArray&gt;
&lt;/molecule&gt;
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