Display partial bonds, eg, transition state

[mcoster]

Just wondering how to display partial bonds, such as in transition state structures? Is this possible using 3Dmol.js?

[dkoes]

Can you provide an example of what this looks like and how it is represented in a molecular file format?

[ghutchis]

My guess is something with dashes/dots/stipple
https://en.wikipedia.org/wiki/Transition_state

[dkoes]

You can add dashed lines:
http://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html#addLine
http://3dmol.csb.pitt.edu/tests/auto/generate_test.cgi?test=test79

Is there a molecular format that encodes these transition state structures and so should display such bonds automatically?

[ghutchis]

There are proposals for supporting zero-order bonds in SDF format, for example.

[mcoster]

The example linked by @ghutchis is what I was thinking of, and addLine seems capable of this.

As far as molecular file formats that can encode this, I am not aware of many. The Jmol wiki suggests that mol and cml can encode partial/0.5 bond order.
http://wiki.jmol.org/index.php/Support_for_bond_orders