Right, thank you, Blaine! It works very well now! Actually there was a problem in the selection from my part so.. I will play with the surfaces a little bit and then will update this topic with my questions :-) Cheers, Enrico
пн, 10 янв. 2022 г. в 16:25, Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>: > > Hi Enrico, > > You do not need the first line of your script. > > This one-liner worked for me in the terminal. > > pymol -c -d > "cmd.fetch('3nd3');cmd.show('surface');cmd.set('transparency','0.5');cmd.save('surf.pse');cmd.png('surf.png')" > > You might test reversing the order of the cmd.png() and cmd.save() commands. > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Associate Professor > Department of Biochemistry and Molecular Biology, College of Medicine > Director of the Laboratory of Biomolecular Structure and Function > Academic Director, Biomolecular Structure Core, COBRE in Structural Biology > Full Member, Cancer Biology Program, Stephenson Cancer Center > University of Oklahoma Health Sciences Center > > Mailing Address: > 975 NE 10th Street, BRC 466 > Oklahoma City, OK 73104-5419 > Office: 405-271-8300 Lab: 405-271-8312 > > Websites: > Faculty page: > https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd > BSC-OKC (LBSF): > https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function > COBRE in Structural Biology: https://www.ou.edu/structuralbiology > ________________________________________ > From: Ali Saad Kusay via PyMOL-users [pymol-users@lists.sourceforge.net] > Sent: Monday, January 10, 2022 8:48 AM > To: Enrico Martinez > Cc: pymol-users > Subject: [EXTERNAL] Re: [PyMOL] surface representation of the protein-ligand > interactions > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Rebuild&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=QM8ZtM6vxjrnYB0Cs6BSV-M8WweuPuuTS1xLMGYQdKU&e= > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_1Of6CNLJyQU0W9yVofmRSV0-3Fdomain-3Dpymol.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=eU60ct3XrRn6e7JdG6JrHLyikGkuUbzJY35JQFXvTv8&e= > > > > You can also try and made the surface more transparent, but this > doesn't always give the best results, see: > https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_vdsUCOMKzVTp8wQ53fvOudq-3Fdomain-3Dpymolwiki.org&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=pOFWGOP750OszaW7BCL8qGLr_VvBCCumHmvodMSYBeo&e= > , 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://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_5uDYCP7LAXfKwZVvQF1Df45-3Fdomain-3Dmail-2Darchive.com&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=f6UjxY4QYDP77HQZ2CqSwjcwA_HDNuyv4cn6nskHIq0&e= > > Unsubscribe: > https://urldefense.proofpoint.com/v2/url?u=https-3A__protect-2Dau.mimecast.com_s_Q3GJCQnMBZfkQ9ZB7FkIfVr-3Fdomain-3Dsourceforge.net&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=lxdjMlSEnLEry730CbGSXWOU9HvpC8iBFjlmcWohToU&e= > > > > > > > > _______________________________________________ > PyMOL-users mailing list > Archives: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=jECdW3kdL8QeZ4l5PxiMhbpjSJBrXPLt0KPxa2kpcwI&e= > Unsubscribe: > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=LJPkRnhTZf8Utg8JOTi736pL_UGe7aSsJfSdAISU1O6habH3BmWqqUuvTrUfXWMh&s=LFkputyTYxDqA2BAGoUDzxEwKZsm3odkMNEHWVV7IZg&e= _______________________________________________ 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