What I've done before is to draw a line between two pseudo-atoms placed
at the center of each ring.
HTH,
Matthew Baumgartner
On 11/10/2015 02:08 AM, Albert wrote:
I think the major concern is how Pymol depicts the pi-pi stacking....
Of course we can identify such interaction immediately as soon as we
open the system in Pymol.
However there is no any components to indicate this, eg: we can
depict the H-bond with a dash between two atoms but how could pi-pi
interaction be depicted?
On 11/10/2015 07:03 AM, Osvaldo Martin wrote:
Hi Amali,
I am not aware that PyMOL has this feature implemented
out-of-the-box. Nevertheless this can be done with PyMOL. A crude
approximation will be to measure the distance between the center of
aromatic rings and consider a pi-pi stacking for distances shorter
than a threshold value. A better model will probably include a
distance threshold and one or two angles in the definition.
Are you trying to estimate pi-pi stacking interactions in general or
for a particular system?
Cheers,
Osvaldo.
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