Thank you for clarification and the fix of the problem.
PM
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.
Bob
On Mon, Aug 4, 2014 at 11:03 PM, Pshemak Maslak <n...@psu.edu
<mailto:n...@psu.edu>> 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?
Thanks,
PM
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 <n...@psu.edu
<mailto:n...@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?
Thanks,
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Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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