From: Ian Stokes-Rees (
Date: Fri Aug 13 2010 - 10:30:15 CDT

On 8/12/10 11:37 PM, Ian Stokes-Rees wrote:
>> If you just wanted to display atom-atom distances, this is a
>> built-in feature.
> That would be fine. Can you give me a hint how to do this?

I've part way figured it out, thanks to the "Comparing Two Structures"
section of the VMD User's Guide:

However the documentation isn't totally clear: I couldn't find an
"Object Mode" pull-down, and there is no "Atom" option directly under
the "Mouse" menu, but trial and error has allowed some progress.

The two problems I now have:

1. How do I get my bond distance to be based on the smoothing window
coordinates rather than the "raw" per-frame coordinates?

2. How do I delete incorrect bond selections, and accidental labels?