Hi Enrico, You can carve the protein surface around the ligand, i.e. show only the surface behind the ligand, see this guide: https://pymol.org/dokuwiki/doku.php?id=figure:carving_surfaces
You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://pymolwiki.org/index.php/Transparency, i.e.: set transparency, 0.5 It would help to see an image of what you are working with atm Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 On 10/1/22, 10:10 pm, "Enrico Martinez" <jmsstarli...@gmail.com> wrote: Dear Pymol users! Working on the vizualisation of the protein-ligand interactions I would like to switch from cartoon to the surface representation of the protein, while still being capable to see the ligand-binding cavity (as well as non-covalent interactions) Could you suggest me some combination of the options which could helps me with such vizualisaiton? I have alread tried show surface, all within 5 of my_pdb and not polymer set surface_smooth_edges, onset surface_smooth_edges, on where my_pdb and not polymer corresponds to the selection of the ligand Eventualy this create cool surface representation of the protein and but completely hides the ligand-binding cavity Many thanks in advance! Enrico _______________________________________________ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/cnxDCMwGxOtqr9lJjhwM0N6?domain=mail-archive.com Unsubscribe: https://protect-au.mimecast.com/s/ZXpPCNLJyQU0W9R6oh42rcB?domain=sourceforge.net _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
