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 soo
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
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
