Thank you for clarification and the fix of the problem.


On 8/5/2014 8:37 AM, Robert Hanson wrote:
It's a bug. Three issues there.

First, the CONTACT command has a bug that makes it only work on the first model.

Second, you probably should be issuing

mySet1={1.6 & _H}; mySet2={1.6 & _H}; contact model 1.6 150% {mySet1} {mySet2}

to display the contact in the proper model.

Third, CONTACT was not set up for allowing "model 1.6" as an option.

That's corrected.

Hope to get that uploaded soon.


On Mon, Aug 4, 2014 at 11:03 PM, Pshemak Maslak <> wrote:
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
$ contact {_O} {_H}

On Tue, May 6, 2014 at 9:43 AM, Pshemak Maslak <> 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?


Infragistics Professional
Build stunning WinForms apps today!
Reboot your WinForms applications with our WinForms controls.
Build a bridge from your legacy apps to the future.
Jmol-users mailing list

Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900