Re: [PyMOL] surface representation of the protein-ligand interactions

[Ali S. K. <aku...@un...>]

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" <jms...@gm...> 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