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

[Enrico M. <jms...@gm...>]

Thank you very much,Ali!
just one question: when I do the surface calculations using bash
script operating with the command lines of the pymol it produces
correctly pse session with the surfaces. BUT if I save an image using
png, the surface is totally absent. Here are my commands directly from
the shell script:

$pymol -c -d "
from pymol import cmd
cmd.load('${results}/${output}_${lig_name}_${receptor}_rep${i}.pdb')
cmd.show( 'surface', '${output}* and polymer within 15 of ${output}*
and not polymer' )
cmd.set( 'transparency', '0.5' )
cmd.save('${vizu}/${output}_${lig_name}_rep${i}.pse')
cmd.png('${vizu}/${output}_${lig_name}_rep${i}.png',width=${image},height=${image},dpi=50,ray=0)
"
As the result of this workflow,  the surface is present in the PSE
file but not in the png image. Otherwise when I save png directly from
the pymol's GUI the surface is well captured on the png as well. What
should I include in my script ?

пн, 10 янв. 2022 г. в 12:18, Ali Saad Kusay <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
>
>
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