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 <akus8...@uni.sydney.edu.au>:
>
> 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
>
>
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