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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