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
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
Dear all,
I want to know can we identify p-p stacking interactions using PyMOL?
Can anyone help me?
Thank you in advance.
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