Hi Enrico, This is beyond my understanding, try and run this bash script without making the surface transparent (to figure out if the issue comes from the transparency)
Also try the rebuild command before saving the image: https://pymolwiki.org/index.php/Rebuild 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, 11:10 pm, "Enrico Martinez" <jmsstarli...@gmail.com> wrote: 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://protect-au.mimecast.com/s/1Of6CNLJyQU0W9yVofmRSV0?domain=pymol.org > > You can also try and made the surface more transparent, but this doesn't always give the best results, see: https://protect-au.mimecast.com/s/vdsUCOMKzVTp8wQ53fvOudq?domain=pymolwiki.org, 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/5uDYCP7LAXfKwZVvQF1Df45?domain=mail-archive.com > Unsubscribe: https://protect-au.mimecast.com/s/Q3GJCQnMBZfkQ9ZB7FkIfVr?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
