I still have problems with "contact" when using butane file containing 20 models (rotamers around the central C-C bond).
Separately, one frame (say gauche) shows contacts fine: contact 100% {_H} {_H},  (net volume 0.14 A^3),  but when that frame is a part (frame 6) of the collection,
something like the following does not work: mySet1={1.6 & _H}; mySet2={1.6 & _H}; contact 100% {mySet1} {mySet2} (net volume 0).

What am I doing wrong?



On 5/6/2014 5:42 PM, Robert Hanson wrote:
Oh, sure. But it's generally designed to ignore intramolecular contacts.

contact {atomset1} {atomset2}

and if {atomset2} is not present, then "same model and not atomset1" is the default.

You can do intramolecular clashes by specifying two distinct intramolecular atom sets.

For example:

$ load caffeine.xyz
$ contact {_O} {_H}

On Tue, May 6, 2014 at 9:43 AM, Pshemak Maslak <nyl@psu.edu> wrote:
Can "contact" command be used to visualize "clashes" in small molecules
(such as eclipsed CH3/CH3 in butane, for example)?

What would the full command look like?