I like the way the Protein-Ligand Interaction Profiler (PLIP, https://projects.biotec.tu-dresden.de/plip-web/plip/index , https://pypi.python.org/pypi/plip , http://nar.oxfordjournals.org/content/early/2015/04/14/nar.gkv315.full ) highlights different interactions in its PyMol output file, such as Pi-Pi stacking, Pi-cation interactions, salt bridges etc. The algorithms and cut-offs used are detailed on the Help page of the server site. It would be nice to be able to apply similar analyses directly in PyMOL, not only to Protein-Ligand(HETATM) interactions, but also to protein-protein interactions.
best regards Annemarie > > 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. >> ------------------------------------------------------------------------------ _______________________________________________ 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
