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
>     >
>     >
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