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. On Tue, Nov 10, 2015 at 5:43 AM, Amali Guruge <amaligg2...@gmail.com> wrote: > Dear all, > > I want to know can we identify p-p stacking interactions using PyMOL? > > Can anyone help me? > > Thank you in advance. > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >
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